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  1. Book: DNA deamination and the immune system

    Fugmann, Sebastian

    aid in health and disease

    (Molecular medicine and medicinal chemistry ; 3)

    2011  

    Author's details ed. by Sebastian Fugmann
    Series title Molecular medicine and medicinal chemistry ; 3
    Collection
    Language English
    Size XIII, 217 S. : Ill.
    Publisher World Scientific
    Publishing place London
    Publishing country Great Britain
    Document type Book
    HBZ-ID HT016463260
    ISBN 978-1-84816-592-2 ; 1-84816-592-7
    Database Catalogue ZB MED Medicine, Health

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  2. Article ; Online: Measuring Mutator Enzyme Activity Using an E. coli-Based Colony Formation Assay.

    Liu, Mei-Chen / Fugmann, Sebastian D

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2421, Page(s) 103–114

    Abstract: Mutator enzymes alter the nucleotide sequences of DNA or RNA molecules; immune systems utilize them to destroy the integrity of pathogen genomes and to optimize immune mediators of the host. Their dysregulation has been linked to tumorigenesis in various ...

    Abstract Mutator enzymes alter the nucleotide sequences of DNA or RNA molecules; immune systems utilize them to destroy the integrity of pathogen genomes and to optimize immune mediators of the host. Their dysregulation has been linked to tumorigenesis in various tissues. Defining and comparing the activities of such mutator enzymes requires a robust versatile assay that is independent of their biological context as in vivo mutation rates are typically low. Here we provide detailed protocols for two widely used E. coli-based approaches that detect the activities of ectopically expressed cytidine deaminases on two distinct reporter genes: an extrachromosomal kanamycin-resistance gene or an endogenous chromosomal substrate, the rpoB gene-encoding RNA polymerase. The generation of mutations is in both cases measured in a colony formation assay. With appropriate modifications, these assays can be extended to study other mutator enzymes.
    MeSH term(s) Cytidine Deaminase/genetics ; DNA ; Escherichia coli/genetics ; Genes, Reporter ; Mutation
    Chemical Substances DNA (9007-49-2) ; Cytidine Deaminase (EC 3.5.4.5)
    Language English
    Publishing date 2021-12-06
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1944-5_7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The cytokine genes of Oncorhynchus masou formosanus include a defective interleukin-4/13A gene.

    Yen, Ying-Hsuan / Zheng, De Yu / Yang, Shu Yuan / Gwo, Jin-Chywan / Fugmann, Sebastian D

    Developmental and comparative immunology

    2024  Volume 155, Page(s) 105156

    Abstract: Oncorhynchus masou formosanus (Formosa landlocked salmon) is a critically endangered salmonid fish endemic to Taiwan. To begin to understand how its drastic change in lifestyle from anadromous to exclusively river-dwelling is reflected in its immune ... ...

    Abstract Oncorhynchus masou formosanus (Formosa landlocked salmon) is a critically endangered salmonid fish endemic to Taiwan. To begin to understand how its drastic change in lifestyle from anadromous to exclusively river-dwelling is reflected in its immune genes, we characterized the genes encoding six cytokines (IL-2A, IL-2B, IL-4/13A, IL-4/13B1, IL-4/13B2, and IL-17A/F2a) important for T cell responses as no genomic data is available for this fish. Interestingly, all genes appeared homozygous indicative of a genetic bottleneck. The IL2 and IL17A/F2a genes and their products are highly similar to their characterized homologs in Oncorhynchus mykiss (rainbow trout) and other salmonid fish. Two notable differences were observed in IL4/13 family important for type 2 immune responses. First, O. m. formosanus carries not only one but two genes encoding IL-4/13B1 proteins and expansions of these genes are present in other salmonid fish. Second, the OmfoIL4/13A gene carries a 228 bp deletion that results in a premature stop codon and hence a non-functional IL-4/13A cytokine. This suggests a reduced ability for T cell responses against parasitic infections in this species.
    MeSH term(s) Animals ; Interleukin-4/genetics ; Interleukin-4/metabolism ; Cytokines/genetics ; Cytokines/metabolism ; Oncorhynchus mykiss ; Genome ; Fish Diseases
    Chemical Substances Interleukin-4 (207137-56-2) ; Cytokines
    Language English
    Publishing date 2024-02-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 752411-0
    ISSN 1879-0089 ; 0145-305X
    ISSN (online) 1879-0089
    ISSN 0145-305X
    DOI 10.1016/j.dci.2024.105156
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Thesis: Interaktionen der Faktoren des V(D)J-Rekombinasekomplexes und Mutationsanalysen der Gamma-c-Ketten und XRCC4-Gene bei Patienten mit schweren kombinierten Immundefekten

    Fugmann, Sebastian

    1997  

    Author's details vorgelegt von Sebastian D. Fugmann
    Language German
    Size 139 Bl. : Ill., graph. Darst.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Ulm, Univ., Diss., 1998
    HBZ-ID HT008880843
    Database Catalogue ZB MED Medicine, Health

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  5. Article ; Online: Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways.

    Hsueh, Shu Wei / Jian, You-Hua / Fugmann, Sebastian D / Yang, Shu Yuan

    PloS one

    2023  Volume 18, Issue 10, Page(s) e0292137

    Abstract: One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including those for polystyrene (PS). Genomics has emerged as a powerful tool for ... ...

    Abstract One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including those for polystyrene (PS). Genomics has emerged as a powerful tool for mining environmental microbes that may have the ability to degrade different types of plastics. In this study, we use 16S rRNA sequencing to analyze the microbiomes for multiple PS samples collected from sites with different vegetation in Taiwan to reveal potential common properties between species that exhibit growth advantages on PS surfaces. Phylum enrichment analysis identified Cyanobacteria and Deinococcus-Thermus as being the most over-represented groups on PS, and both phyla include species known to reside in extreme environments and could encode unique enzymes that grant them properties suitable for colonization on PS surfaces. Investigation of functional enrichment using reference genomes of PS-enriched species highlighted carbon metabolic pathways, especially those related to hydrocarbon degradation. This is corroborated by the finding that genes encoding long-chain alkane hydroxylases such as AlmA are more prevalent in the genomes of PS-associated bacteria. Our analyses illustrate how plastic in the environment support the colonization by different microbes compared to surrounding soil. In addition, our results point to the possibility that alkane hydroxylases could confer growth advantages of microbes on PS.
    MeSH term(s) Polystyrenes ; Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria ; Biodegradation, Environmental ; Mixed Function Oxygenases ; Alkanes/metabolism
    Chemical Substances Polystyrenes ; Plastics ; RNA, Ribosomal, 16S ; Mixed Function Oxygenases (EC 1.-) ; Alkanes
    Language English
    Publishing date 2023-10-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0292137
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  6. Article ; Online: Functional characterization of the MyD88 homologs in Strongylocentrotus purpuratus.

    Chou, Shu-Ting / Lin, Tse-Mao / Yang, Huang-Yu / Fugmann, Sebastian D

    Developmental and comparative immunology

    2022  Volume 139, Page(s) 104580

    Abstract: Toll-like receptor signaling is an evolutionarily conserved pathway to induce the expression of immune mediators in response to encounters with pathogens. MyD88 is a central adapter connecting the intracellular domain of the receptors to downstream ... ...

    Abstract Toll-like receptor signaling is an evolutionarily conserved pathway to induce the expression of immune mediators in response to encounters with pathogens. MyD88 is a central adapter connecting the intracellular domain of the receptors to downstream kinases. Here, we conducted a comprehensive assessment of the MyD88 family in an echinoderm, Strongylocentrotus purpuratus. Of five SpMyD88s only two closely related proteins, SpMyD88A and SpMyD88B, are functional in mammalian cell lines as their overexpression facilitates the activation of the downstream transcription factor NF-κB. This requires the presence of the endogenous mammalian MyD88s, and domain swapping indicated that the death domains of S. purpuratus MyD88 are unable to efficiently connect to the respective domains of the vertebrate IRAK kinases. This suggests that the interaction surfaces between the signaling mediators in this conserved signaling pathway are not as conserved as previously thought but were likely shaped and evolved by pathogenic selection over evolutionary timescales.
    MeSH term(s) Animals ; Strongylocentrotus purpuratus/genetics ; Mammals
    Language English
    Publishing date 2022-10-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 752411-0
    ISSN 1879-0089 ; 0145-305X
    ISSN (online) 1879-0089
    ISSN 0145-305X
    DOI 10.1016/j.dci.2022.104580
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  7. Article ; Online: Form follows function - the three-dimensional structure of antigen receptor gene loci.

    Fugmann, Sebastian D

    Current opinion in immunology

    2014  Volume 27, Page(s) 33–37

    Abstract: ... by a somatic gene rearrangement process named V(D)J recombination. This process is tightly regulated to ensure ... to ensure the appropriate access of the V(D)J recombinase machinery at each developmental stage, and ...

    Abstract Antigen receptor genes are assembled during lymphocyte development from individual gene segments by a somatic gene rearrangement process named V(D)J recombination. This process is tightly regulated to ensure the generation of an unbiased broad primary repertoire of immunoglobulins and T cell receptors, and to prevent aberrant recombination products that could initiate lymphomagenesis. One important mode of regulation that has recently been discovered for the immunoglobulin heavy chain (IGH) gene locus is the adoption of distinct three-dimensional structures of the locus. Changes in the spatial conformation are thought to ensure the appropriate access of the V(D)J recombinase machinery at each developmental stage, and the formation of extensive chromosome loops has been implicated in allowing equal access to widely dispersed gene elements.
    MeSH term(s) Animals ; Genetic Loci ; Humans ; Immunoglobulins/genetics ; Immunoglobulins/immunology ; Nucleic Acid Conformation ; Receptors, Antigen/chemistry ; Receptors, Antigen/genetics ; Receptors, Antigen/immunology ; V(D)J Recombination
    Chemical Substances Immunoglobulins ; Receptors, Antigen
    Language English
    Publishing date 2014-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1035767-1
    ISSN 1879-0372 ; 0952-7915
    ISSN (online) 1879-0372
    ISSN 0952-7915
    DOI 10.1016/j.coi.2014.01.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Lectins identify distinct populations of coelomocytes in Strongylocentrotus purpuratus.

    Liao, Wen-Yun / Fugmann, Sebastian D

    PloS one

    2017  Volume 12, Issue 11, Page(s) e0187987

    Abstract: Coelomocytes represent the immune cells of echinoderms, but detailed knowledge about their roles during immune responses is very limited. One major challenge for studying coelomocyte biology is the lack of reagents to identify and purify distinct ... ...

    Abstract Coelomocytes represent the immune cells of echinoderms, but detailed knowledge about their roles during immune responses is very limited. One major challenge for studying coelomocyte biology is the lack of reagents to identify and purify distinct populations defined by objective molecular markers rather than by morphology-based classifications that are subjective at times. Glycosylation patterns are known to differ significantly between cell types in vertebrates, and furthermore they can vary depending on the developmental stage and activation states within a given lineage. Thus fluorescently labeled lectins that recognize distinct glycan structures on cell surface proteins are routinely used to identify discrete cell populations in the vertebrate immune system. Here we now employed a panel of fifteen fluorescently-labeled lectins to determine differences in the glycosylation features on the surface of Strongylocentrotus purpuratus coelomocytes by fluorescence microscopy and flow cytometry. Eight of the lectins (succinylated wheat germ agglutinin, Len culinaris lectin, Pisum sativum agglutinin, Saphora japonica agglutinin, Solanum tuberosum lectin, Lycopersicon esculentum lectin, Datura stramonium lectin, Vicia villosa lectin) showed distinct binding patterns to fixed and live cells of three major coelomocyte classes: phagocytic cells, red spherule cells, and vibratile cells. Importantly, almost all lectins bound only to a subgroup of cells within each cell type. Lastly, we established fluorescently-labeled lectin-based fluorescence activated cell sorting as a strategy to purify distinct S. purpuratus coelomocyte (sub-)populations based on molecular markers. We anticipate that this will become a routine approach in future studies focused on dissecting the roles of different coelomocytes in echinoderm immunity.
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0187987
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Deficiency of activation-induced cytidine deaminase in a murine model of ulcerative colitis

    Laura P. Hale / Sebastian D. Fugmann

    PLoS ONE, Vol 15, Iss

    2020  Volume 9

    Abstract: Patients with inflammatory bowel disease (IBD) have an increased risk of colorectal cancer, particularly in ulcerative colitis (UC) when the majority of colon epithelial cells may be exposed to inflammation-associated mutagenesis. In addition to ... ...

    Abstract Patients with inflammatory bowel disease (IBD) have an increased risk of colorectal cancer, particularly in ulcerative colitis (UC) when the majority of colon epithelial cells may be exposed to inflammation-associated mutagenesis. In addition to mutagenesis generated by oxidative stress, inflammation can induce activation-induced cytidine deaminase (Aicda), a mutator enzyme in the APOBEC family, within colon epithelial cells. This study tested the hypothesis that deletion of the Aicda gene could protect against the development of inflammation-associated colorectal cancers, using a model of UC-like colitis in “T/I” mice deficient in TNF and IL10. Results showed that T/I mice that were additionally Aicda-deficient (“TIA” mice) spontaneously developed moderate to severe UC-like colitis soon after weaning, with histologic features and colon inflammation severity scores similar those in T/I mice. Although the mean survival of TIA mice was decreased compared to T/I mice, multivariable analysis that adjusted for age when neoplasia was ascertained showed a decreased numbers of neoplastic colorectal lesions in TIA mice, with a trend toward decreased incidence of neoplasia. Aicda deficiency increased serum IL1α and slightly decreased IL12p40 and M-CSF, as compared with T/I mice, and led to undetectable levels of IgA, IgG1, IgG2a, IgG2b, and IgG3. Taken together, these studies show that Aicda deficiency can decrease the number of neoplastic lesions but is not sufficient to prevent the risk of inflammation-associated colorectal neoplasia in the setting of severe UC-like inflammation. The TIA model may also be useful for assessing the roles of antibody class-switch recombination deficiency and somatic hypermutation on regulation of microbiota and inflammation in the small intestine and colon, as well as the pathogenesis of colitis associated with hyper-IgM syndrome in humans. Further studies will be required to determine the mechanisms that drive early mortality in TIA mice.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: RAG-2 unleashed: lymphocytes beware.

    Fugmann, Sebastian D

    Immunity

    2011  Volume 34, Issue 2, Page(s) 137–139

    Abstract: The programmed degradation of the RAG-2 enzyme upon entry to S phase restricts V(D)J recombination ...

    Abstract The programmed degradation of the RAG-2 enzyme upon entry to S phase restricts V(D)J recombination to the G0-G1 phase of the cell cycle. In this issue of Immunity, Zhang et al. (2011) show that this is critical to prevent lymphoma formation.
    Language English
    Publishing date 2011-02-22
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 1217235-2
    ISSN 1097-4180 ; 1074-7613
    ISSN (online) 1097-4180
    ISSN 1074-7613
    DOI 10.1016/j.immuni.2011.02.007
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