{"entity": "journal", "iuid": "15c686b02a4046bfb30e17ee44a1f1df", "timestamp": "2026-07-17T09:08:18.485Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Glycobiology.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Glycobiology"}}, "title": "Glycobiology", "issn": "1460-2423", "issn-l": "0959-6658", "publications_count": 10, "publications": [{"entity": "publication", "iuid": "a10a0bc7212345da8ed7dd412b671eff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a10a0bc7212345da8ed7dd412b671eff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a10a0bc7212345da8ed7dd412b671eff"}}, "title": "N-glycoproteomic analyses of human intestinal enteroids, varying in histo-blood group geno- and phenotypes, reveal a wide repertoire of fucosylated glycoproteins.", "authors": [{"family": "Nilsson", "given": "Jonas", "initials": "J"}, {"family": "Rimkute", "given": "Inga", "initials": "I"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Tenge", "given": "Victoria R", "initials": "VR"}, {"family": "Lin", "given": "Shih-Ching", "initials": "SC"}, {"family": "Atmar", "given": "Robert L", "initials": "RL"}, {"family": "Estes", "given": "Mary K", "initials": "MK"}, {"family": "Larson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-2616-0366", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a940eae9164c56a1d2f9b8ef8242cd.json"}}], "type": "journal article", "published": "2024-04-24", "journal": {"title": "Glycobiology", "issn": "1460-2423", "volume": "34", "issue": "6", "issn-l": "0959-6658"}, "abstract": "Human noroviruses, globally the main cause of viral gastroenteritis, show strain specific affinity for histo-blood group antigens (HBGA) and can successfully be propagated ex vivo in human intestinal enteroids (HIEs). HIEs established from jejunal stem cells of individuals with different ABO, Lewis and secretor geno- and phenotypes, show varying susceptibility to such infections. Using bottom-up glycoproteomic approaches we have defined and compared the N-linked glycans of glycoproteins of seven jejunal HIEs. Membrane proteins were extracted, trypsin digested, and glycopeptides enriched by hydrophilic interaction liquid chromatography and analyzed by nanoLC-MS/MS. The Byonic software was used for glycopeptide identification followed by hands-on verifications and interpretations. Glycan structures and attachment sites were identified from MS2 spectra obtained by higher-energy collision dissociation through analysis of diagnostic saccharide oxonium ions (B-ions), stepwise glycosidic fragmentation of the glycans (Y-ions), and peptide sequence ions (b- and y-ions). Altogether 694 unique glycopeptides from 93 glycoproteins were identified. The N-glycans encompassed pauci- and oligomannose, hybrid- and complex-type structures. Notably, polyfucosylated HBGA-containing glycopeptides of the four glycoproteins tetraspanin-8, carcinoembryonic antigen-related cell adhesion molecule 5, sucrose-isomaltase and aminopeptidase N were especially prominent and were characterized in detail and related to donor ABO, Lewis and secretor types of each HIE. Virtually no sialylated N-glycans were identified for these glycoproteins suggesting that terminal sialylation was infrequent compared to fucosylation and HBGA biosynthesis. This approach gives unique site-specific information on the structural complexity of N-linked glycans of glycoproteins of human HIEs and provides a platform for future studies on the role of host glycoproteins in gastrointestinal infectious diseases.", "doi": "10.1093/glycob/cwae029", "pmid": "38590172", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11041853"}, {"db": "pii", "key": "7642527"}], "notes": [], "created": "2024-09-15T11:28:40.665Z", "modified": "2024-11-27T15:30:45.001Z"}, {"entity": "publication", "iuid": "f4fb4e1feff8482297a0ef22848d569c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4fb4e1feff8482297a0ef22848d569c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4fb4e1feff8482297a0ef22848d569c"}}, "title": "Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck.", "authors": [{"family": "Nilsson", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Naguib", "given": "Mahmoud M", "initials": "MM"}, {"family": "Jax", "given": "Elinor", "initials": "E"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Olsson", "given": "Britt-Marie", "initials": "BM"}, {"family": "Lundkvist", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Olsen", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "J\u00e4rhult", "given": "Josef D", "initials": "JD"}, {"family": "Larson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-2616-0366", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a940eae9164c56a1d2f9b8ef8242cd.json"}}, {"family": "Ellstr\u00f6m", "given": "Patrik", "initials": "P", "orcid": "0000-0001-8920-6061", "researcher": {"href": "https://publications.scilifelab.se/researcher/28d0078ecd884b73a546ca84bec90127.json"}}], "type": "journal article", "published": "2024-04-01", "journal": {"title": "Glycobiology", "issn": "1460-2423", "issn-l": "0959-6658", "volume": "34", "issue": "3", "pages": null}, "abstract": "Influenza A virus (IAV) pandemics result from interspecies transmission events within the avian reservoir and further into mammals including humans. Receptor incompatibility due to differently expressed glycan structures between species has been suggested to limit zoonotic IAV transmission from the wild bird reservoir as well as between different bird species. Using glycoproteomics, we have studied the repertoires of expressed glycan structures with focus on putative sialic acid-containing glycan receptors for IAV in mallard, chicken and tufted duck; three bird species with different roles in the zoonotic ecology of IAV. The methodology used pinpoints specific glycan structures to specific glycosylation sites of identified glycoproteins and was also used to successfully discriminate \u03b12-3- from \u03b12-6-linked terminal sialic acids by careful analysis of oxonium ions released from glycopeptides in tandem MS/MS (MS2), and MS/MS/MS (MS3). Our analysis clearly demonstrated that all three bird species can produce complex N-glycans including \u03b12-3-linked sialyl Lewis structures, as well as both N- and O- glycans terminated with both \u03b12-3- and \u03b12-6-linked Neu5Ac. We also found the recently identified putative IAV receptor structures, Man-6P N-glycopeptides, in all tissues of the three bird species. Furthermore, we found many similarities in the repertoires of expressed receptors both between the bird species investigated and to previously published data from pigs and humans. Our findings of sialylated glycan structures, previously anticipated to be mammalian specific, in all three bird species may have major implications for our understanding of the role of receptor incompatibility in interspecies transmission of IAV.", "doi": "10.1093/glycob/cwad098", "pmid": "38127648", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10987293"}, {"db": "pii", "key": "7486526"}], "notes": [], "created": "2024-01-09T14:53:01.557Z", "modified": "2024-11-27T15:30:43.725Z"}, {"entity": "publication", "iuid": "c3946fe3e96345d4879afb8cce47d2b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3946fe3e96345d4879afb8cce47d2b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3946fe3e96345d4879afb8cce47d2b4"}}, "title": "Characterization of the ganglioside recognition profile of Escherichia coli heat-labile enterotoxin LT-IIc.", "authors": [{"family": "Zalem", "given": "Dani", "initials": "D"}, {"family": "Juh\u00e1s", "given": "Martin", "initials": "M"}, {"family": "Terrinoni", "given": "Manuela", "initials": "M"}, {"family": "King-Lyons", "given": "Natalie", "initials": "N"}, {"family": "Lebens", "given": "Michael", "initials": "M"}, {"family": "Varrot", "given": "Annabelle", "initials": "A"}, {"family": "Connell", "given": "Terry D", "initials": "TD"}, {"family": "Teneberg", "given": "Susann", "initials": "S", "orcid": "0000-0003-1957-9553", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e79099e3fe4398a6b030896efb7308.json"}}], "type": "journal article", "published": "2022-04-21", "journal": {"title": "Glycobiology", "issn": "1460-2423", "volume": "32", "issue": "5", "pages": "391-403", "issn-l": "0959-6658"}, "abstract": "The heat-labile enterotoxins of Escherichia coli and cholera toxin of Vibrio cholerae are related in structure and function. Each of these oligomeric toxins is comprised of one A polypeptide and five B polypeptides. The B-subunits bind to gangliosides, which are followed by uptake into the intoxicated cell and activation of the host's adenylate cyclase by the A-subunits. There are two antigenically distinct groups of these toxins. Group I includes cholera toxin and type I heat-labile enterotoxin of E. coli; group II contains the type II heat-labile enterotoxins of E. coli. Three variants of type II toxins, designated LT-IIa, LT-IIb and LT-IIc have been described. Earlier studies revealed the crystalline structure of LT-IIb. Herein the carbohydrate binding specificity of LT-IIc B-subunits was investigated by glycosphingolipid binding studies on thin-layer chromatograms and in microtiter wells. Binding studies using a large variety of glycosphingolipids showed that LT-IIc binds with high affinity to gangliosides with a terminal Neu5Ac\u03b13Gal or Neu5Gc\u03b13Gal, e.g. the gangliosides GM3, GD1a and Neu5Ac\u03b13-/Neu5Gc\u03b13--neolactotetraosylceramide and Neu5Ac\u03b13-/Neu5Gc\u03b13-neolactohexaosylceramide. The crystal structure of LT-IIc B-subunits alone and with bound LSTd/sialyl-lacto-N-neotetraose d pentasaccharide uncovered the molecular basis of the ganglioside recognition. These studies revealed common and unique functional structures of the type II family of heat-labile enterotoxins.", "doi": "10.1093/glycob/cwab133", "pmid": "34972864", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9022906"}, {"db": "pii", "key": "6482028"}], "notes": [], "created": "2022-11-30T12:04:15.224Z", "modified": "2024-01-16T13:46:29.258Z"}, {"entity": "publication", "iuid": "ffe2c444add84a2597feb065a5b6f4ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffe2c444add84a2597feb065a5b6f4ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffe2c444add84a2597feb065a5b6f4ac"}}, "title": "Proteoglycan profiling of human, rat and mouse insulin-secreting cells.", "authors": [{"family": "Nikpour", "given": "Mahnaz", "initials": "M"}, {"family": "Nilsson", "given": "Jonas", "initials": "J"}, {"family": "Persson", "given": "Andrea", "initials": "A"}, {"family": "Noborn", "given": "Fredrik", "initials": "F"}, {"family": "Vorontsov", "given": "Egor", "initials": "E"}, {"family": "Larson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-2616-0366", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a940eae9164c56a1d2f9b8ef8242cd.json"}}], "type": "journal article", "published": "2021-09-09", "journal": {"title": "Glycobiology", "issn": "1460-2423", "volume": "31", "issue": "8", "pages": "916-930", "issn-l": "0959-6658"}, "abstract": "Proteoglycans (PGs) are proteins with glycosaminoglycan (GAG) chains, such as chondroitin sulfate (CS) or heparan sulfate (HS), attached to serine residues. We have earlier shown that prohormones can carry CS, constituting a novel class of PGs. The mapping of GAG modifications of proteins in endocrine cells may thus assist us in delineating possible roles of PGs in endocrine cellular physiology. With this aim, we applied a glycoproteomic approach to identify PGs, their GAG chains and their attachment sites in insulin-secreting cells. Glycopeptides carrying GAG chains were enriched from human pancreatic islets, rat (INS-1 832/13) and mouse (MIN6, NIT-1) insulinoma cell lines by exchange chromatography, depolymerized with GAG lyases, and analyzed by nanoflow liquid chromatography tandem mass spectrometry. We identified CS modifications of chromogranin-A (CgA), islet amyloid polypeptide, secretogranin-1 and secretogranin-2, immunoglobulin superfamily member 10, and protein AMBP. Additionally, we identified two HS-modified prohormones (CgA and secretogranin-1), which was surprising, as prohormones are not typically regarded as HSPGs. For CgA, the glycosylation site carried either CS or HS, making it a so-called hybrid site. Additional HS sites were found on syndecan-1, syndecan-4, nerurexin-2, protein NDNF and testican-1. These results demonstrate that several prohormones, and other constituents of the insulin-secreting cells are PGs. Cell-targeted mapping of the GAG glycoproteome forms an important basis for better understanding of endocrine cellular physiology, and the novel CS and HS sites presented here provide important knowledge for future studies.", "doi": "10.1093/glycob/cwab035", "pmid": "33997891", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8434799"}, {"db": "pii", "key": "6274761"}], "notes": [], "created": "2021-12-09T21:09:03.428Z", "modified": "2024-01-16T13:46:30.174Z"}, {"entity": "publication", "iuid": "26470c69495642ceafe35babf6c55ec2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26470c69495642ceafe35babf6c55ec2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26470c69495642ceafe35babf6c55ec2"}}, "title": "Inhibition of iduronic acid biosynthesis by ebselen reduces GAG accumulation in MPS-I fibroblasts.", "authors": [{"family": "Maccarana", "given": "Marco", "initials": "M", "orcid": "0000-0003-3549-8921", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a0ad51ef8544edebfb4d05227179a35.json"}}, {"family": "Tykesson", "given": "Emil", "initials": "E", "orcid": "0000-0002-0511-9831", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd615245d50b47639f38f55fbf3f4fe3.json"}}, {"family": "Pera", "given": "Edgar M", "initials": "EM"}, {"family": "Gouignard", "given": "Nad\u00e8ge", "initials": "N"}, {"family": "Fang", "given": "Jianping", "initials": "J", "orcid": "0000-0002-1695-2693", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b7388d3c88d4c20acf059e28fe0ea42.json"}}, {"family": "Malmstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0002-6691-146X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c756d46971f4670abdb5faafb10ad56.json"}}, {"family": "Ghiselli", "given": "Giancarlo", "initials": "G"}, {"family": "Li", "given": "Jin-Ping", "initials": "J"}], "type": "journal article", "published": "2021-06-29", "journal": {"title": "Glycobiology", "issn": "1460-2423", "issn-l": "0959-6658", "volume": null, "issue": null, "pages": null}, "abstract": "Mucopolysaccharidosis type one (MPS-I) is a rare lysosomal storage disorder caused by deficiency of the enzyme alpha-L-iduronidase which removes iduronic acid in both chondroitin/dermatan sulfate (CS/DS) and heparan sulfate (HS) and thereby contributes to the catabolism of glycosaminoglycans (GAGs). To ameliorate this genetic defect, the patients are currently treated by enzyme replacement and bone marrow transplantation, which have a number of drawbacks. This study was designed to develop an alternative treatment by inhibition of iduronic acid formation. By screening the Prestwick drug library, we identified ebselen as a potent inhibitor of enzymes that produce iduronic acid in CS/DS and HS. Ebselen efficiently inhibited iduronic acid formation during CS/DS synthesis in cultured fibroblasts. Treatment of MPS-I fibroblasts with ebselen not only reduced accumulation of CS/DS, but also promoted GAG degradation. In early Xenopus embryos, this drug phenocopied the effect of downregulation of DS-epimerase 1, the main enzyme responsible for iduronic production in CS/DS, suggesting that ebselen inhibits iduronic acid production in vivo. However, ebselen failed to ameliorate the CS/DS and GAG burden in MPS-I mice. Nevertheless, the results propose a potential of iduronic acid substrate reduction therapy for MPS-I patients.", "doi": "10.1093/glycob/cwab066", "pmid": "34192316", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "6311239"}], "notes": [], "created": "2021-11-18T07:49:14.353Z", "modified": "2025-10-17T13:04:28.090Z"}, {"entity": "publication", "iuid": "b7d0da972959431b9c6cf7e087a13774", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7d0da972959431b9c6cf7e087a13774.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7d0da972959431b9c6cf7e087a13774"}}, "title": "Recombinant dermatan sulfate is a potent activator of heparin cofactor II-dependent inhibition of thrombin.", "authors": [{"family": "Tykesson", "given": "Emil", "initials": "E", "orcid": "0000-0002-0511-9831", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd615245d50b47639f38f55fbf3f4fe3.json"}}, {"family": "Maccarana", "given": "Marco", "initials": "M"}, {"family": "Thorsson", "given": "Hanna", "initials": "H"}, {"family": "Liu", "given": "Jian", "initials": "J"}, {"family": "Malmstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Ellervik", "given": "Ulf", "initials": "U"}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G"}], "type": "journal article", "published": "2019-06-01", "journal": {"issn": "1460-2423", "volume": "29", "issue": "6", "pages": "446-451", "title": "Glycobiology", "issn-l": "0959-6658"}, "abstract": "The glycosaminoglycan dermatan sulfate (DS) is a well-known activator of heparin cofactor II-dependent inactivation of thrombin. In contrast to heparin, dermatan sulfate has never been prepared recombinantly from material of non-animal origin. Here we report on the enzymatic synthesis of structurally well-defined DS with high anticoagulant activity. Using a microbial K4 polysaccharide and the recombinant enzymes DS-epimerase 1, dermatan 4-O-sulfotransferase 1, uronyl 2-O-sulfotransferase and N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase, several new glycostructures have been prepared, such as a homogenously sulfated IdoA-GalNAc-4S polymer and its 2-O-, 6-O- and 2,6-O-sulfated derivatives. Importantly, the recombinant highly 2,4-O-sulfated DS inhibits thrombin via heparin cofactor II, approximately 20 times better than heparin, enabling manipulation of vascular and extravascular coagulation. The potential of this method can be extended to preparation of specific structures that are of importance for binding and activation of cytokines, and control of inflammation and metastasis, involving extravasation and migration.", "doi": "10.1093/glycob/cwz019", "pmid": "30869126", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7008404"}, {"db": "pii", "key": "5380615"}], "notes": [], "created": "2023-05-31T16:28:11.332Z", "modified": "2025-10-17T13:03:57.834Z"}, {"entity": "publication", "iuid": "0aef3c597a604f378c0bff70cd9aa128", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0aef3c597a604f378c0bff70cd9aa128.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0aef3c597a604f378c0bff70cd9aa128"}}, "title": "Identification of a non-canonical chondroitin sulfate linkage region trisaccharide.", "authors": [{"family": "Persson", "given": "Andrea", "initials": "A"}, {"family": "Nilsson", "given": "Jonas", "initials": "J"}, {"family": "Vorontsov", "given": "Egor", "initials": "E"}, {"family": "Noborn", "given": "Fredrik", "initials": "F"}, {"family": "Larson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2019-05-01", "journal": {"title": "Glycobiology", "issn": "1460-2423", "volume": "29", "issue": "5", "pages": "366-371", "issn-l": "0959-6658"}, "abstract": "It is generally accepted that the biosynthesis of chondroitin sulfate and heparan sulfate is proceeding from a common linkage region tetrasaccharide comprising GlcA-Gal-Gal-Xyl-O-. The linkage region can undergo various modifications such as sulfation, phosphorylation and sialylation, and as the methods for studying glycosaminoglycan structure have been developed and refined, the number of discovered modifications has increased. Previous studies on the linkage region and the glycosyltransferases involved in the biosynthesis suggest that variants of the linkage region tetrasaccharide may also be possible. Here, using LC-MS/MS, we describe a non-canonical linkage region trisaccharide comprising GlcA-Gal-Xyl-O-. The trisaccharide was identified as a minor constituent in the proteoglycan bikunin from urine of human healthy donors present as a disulfated pentasaccharide, \u0394HexA-GalNAc(S)-GlcA-Gal(S)-Xyl-O-, after chondroitinase ABC degradation. Furthermore, it was present as the corresponding disulfated pentasaccharide after chondroitinase ABC degradation in chondroitin sulfate primed on xylosides isolated from human cell lines. This linkage region trisaccharide may serve as an alternative point of entry for glycosaminoglycan biosynthesis.", "doi": "10.1093/glycob/cwz014", "pmid": "30824935", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5368387"}], "notes": [], "created": "2020-01-30T15:57:25.713Z", "modified": "2024-01-16T13:46:31.765Z"}, {"entity": "publication", "iuid": "23d5b7c33105443e802947adc403df94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23d5b7c33105443e802947adc403df94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23d5b7c33105443e802947adc403df94"}}, "title": "GlyTouCan: an accessible glycan structure repository.", "authors": [{"family": "Tiemeyer", "given": "Michael", "initials": "M"}, {"family": "Aoki", "given": "Kazuhiro", "initials": "K"}, {"family": "Paulson", "given": "James", "initials": "J"}, {"family": "Cummings", "given": "Richard D", "initials": "RD"}, {"family": "York", "given": "William S", "initials": "WS"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Lisacek", "given": "Frederique", "initials": "F"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "Campbell", "given": "Matthew P", "initials": "MP"}, {"family": "Aoki", "given": "Nobuyuki P", "initials": "NP"}, {"family": "Fujita", "given": "Akihiro", "initials": "A"}, {"family": "Matsubara", "given": "Masaaki", "initials": "M"}, {"family": "Shinmachi", "given": "Daisuke", "initials": "D"}, {"family": "Tsuchiya", "given": "Shinichiro", "initials": "S"}, {"family": "Yamada", "given": "Issaku", "initials": "I"}, {"family": "Pierce", "given": "Michael", "initials": "M"}, {"family": "Ranzinger", "given": "Ren\u00e9", "initials": "R"}, {"family": "Narimatsu", "given": "Hisashi", "initials": "H"}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "27", "issn": "1460-2423", "issue": "10", "pages": "915-919", "title": "Glycobiology", "issn-l": "0959-6658"}, "abstract": "Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.", "doi": "10.1093/glycob/cwx066", "pmid": "28922742", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4079955"}, {"db": "pmc", "key": "PMC5881658"}], "notes": [], "created": "2020-01-30T16:19:35.484Z", "modified": "2024-01-16T13:46:32.482Z"}, {"entity": "publication", "iuid": "07bf66914419434180e929e4cb7416c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07bf66914419434180e929e4cb7416c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07bf66914419434180e929e4cb7416c0"}}, "title": "Epitope mapping of a new anti-Tn antibody detecting gastric cancer cells.", "authors": [{"family": "Persson", "given": "Nina", "initials": "N"}, {"family": "Stuhr-Hansen", "given": "Nicolai", "initials": "N"}, {"family": "Risinger", "given": "Christian", "initials": "C"}, {"family": "Mereiter", "given": "Stefan", "initials": "S"}, {"family": "Pol\u00f3nia", "given": "Ant\u00f3nio", "initials": "A"}, {"family": "Polom", "given": "Karol", "initials": "K"}, {"family": "Kov\u00e1cs", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Roviello", "given": "Franco", "initials": "F"}, {"family": "Reis", "given": "Celso A", "initials": "CA"}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Danielsson", "given": "Lena", "initials": "L"}, {"family": "Jansson", "given": "Bo", "initials": "B"}, {"family": "Blixt", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2017-07-01", "journal": {"title": "Glycobiology", "issn": "1460-2423", "volume": "27", "issue": "7", "pages": "635-645", "issn-l": "0959-6658"}, "abstract": "Here, we introduce a novel scFv antibody, G2-D11, specific for two adjacent Tn-antigens (GalNAc-Ser/Thr) binding equally to three dimeric forms of the epitope, Ser-Thr, Thr-Thr and Thr-Ser. Compared to other anti-Tn reagents, the binding of G2-D11 is minimally influenced by the peptide structure, which indicates a high degree of carbohydrate epitope dominance and a low influence from the protein backbone. With a high affinity (KDapp = 1.3 \u00d7 10-8 M) and no cross-reactivity to either sialyl-Tn epitope or blood group A antigens, scFv G2-D11 is an excellent candidate for a well-defined anti-Tn-antigen reagent. Detailed immunohistochemical evaluation of tissue sections from a cohort of 80 patients with gastric carcinoma showed in all cases positive tumor cells. The observed staining was localized to the cytoplasm and in some cases to the membrane, whereas the surrounding tissue was completely negative demonstrating the usefulness of the novel Tn-antigen binding antibody.", "doi": "10.1093/glycob/cwx033", "pmid": "28419225", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "3611453"}], "notes": [], "created": "2020-01-27T10:10:40.886Z", "modified": "2021-05-24T15:39:50.116Z"}, {"entity": "publication", "iuid": "fa9dc30e92324f51a6af8689a8b622fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa9dc30e92324f51a6af8689a8b622fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa9dc30e92324f51a6af8689a8b622fc"}}, "title": "The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data.", "authors": [{"family": "Liu", "given": "Yan", "initials": "Y"}, {"family": "McBride", "given": "Ryan", "initials": "R"}, {"family": "Stoll", "given": "Mark", "initials": "M"}, {"family": "Palma", "given": "Angelina S", "initials": "AS"}, {"family": "Silva", "given": "Lisete", "initials": "L"}, {"family": "Agravat", "given": "Sanjay", "initials": "S"}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF"}, {"family": "Campbell", "given": "Matthew P", "initials": "MP"}, {"family": "Costello", "given": "Catherine E", "initials": "CE"}, {"family": "Dell", "given": "Anne", "initials": "A"}, {"family": "Haslam", "given": "Stuart M", "initials": "SM"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Khoo", "given": "Kay-Hooi", "initials": "KH"}, {"family": "Kolarich", "given": "Daniel", "initials": "D"}, {"family": "Novotny", "given": "Milos V", "initials": "MV"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "Ranzinger", "given": "Rene", "initials": "R"}, {"family": "Rapp", "given": "Erdmann", "initials": "E"}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}, {"family": "Struwe", "given": "Weston B", "initials": "WB"}, {"family": "Tiemeyer", "given": "Michael", "initials": "M"}, {"family": "Wells", "given": "Lance", "initials": "L"}, {"family": "York", "given": "William S", "initials": "WS"}, {"family": "Zaia", "given": "Joseph", "initials": "J"}, {"family": "Kettner", "given": "Carsten", "initials": "C"}, {"family": "Paulson", "given": "James C", "initials": "JC"}, {"family": "Feizi", "given": "Ten", "initials": "T"}, {"family": "Smith", "given": "David F", "initials": "DF"}], "type": "editorial", "published": "2017-04-00", "journal": {"volume": "27", "issn": "1460-2423", "issue": "4", "pages": "280-284", "title": "Glycobiology", "issn-l": "0959-6658"}, "abstract": "MIRAGE (Minimum Information Required for A Glycomics Experiment) is an initiative that was created by experts in the fields of glycobiology, glycoanalytics and glycoinformatics to produce guidelines for reporting results from the diverse types of experiments and analyses used in structural and functional studies of glycans in the scientific literature. As a sequel to the guidelines for sample preparation (Struwe et al. 2016, Glycobiology, 26:907-910) and mass spectrometry data (Kolarich et al. 2013, Mol. Cell Proteomics, 12:991-995), here we present the first version of guidelines intended to improve the standards for reporting data from glycan microarray analyses. For each of eight areas in the workflow of a glycan microarray experiment, we provide guidelines for the minimal information that should be provided in reporting results. We hope that the MIRAGE glycan microarray guidelines proposed here will gain broad acceptance by the community, and will facilitate interpretation and reproducibility of the glycan microarray results with implications in comparison of data from different laboratories and eventual deposition of glycan microarray data in international databases.", "doi": "10.1093/glycob/cww118", "pmid": "27993942", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "cww118"}, {"db": "pmc", "key": "PMC5444268"}], "notes": [], "created": "2020-01-30T16:19:32.804Z", "modified": "2024-01-16T13:46:32.762Z"}], "created": "2020-01-27T10:10:40.899Z", "modified": "2020-11-27T13:14:02.961Z"}