| 1. |
- Liu, Y., et al.
(författare)
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The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data
- 2017
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 27:4, s. 280-284
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Tidskriftsartikel (refereegranskat)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.
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| 2. |
- York, W. S., et al.
(författare)
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MIRAGE: The minimum information required for a glycomics experiment
- 2014
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 24:5, s. 402-406
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Tidskriftsartikel (refereegranskat)abstract
- The MIRAGE (minimum information required for a glycomics experiment) initiative was founded in Seattle, WA, in November 2011 in order to develop guidelines for reporting the qualitative and quantitative results obtained by diverse types of glycomics analyses, including the conditions and techniques that were applied to prepare the glycans for analysis and generate the primary data along with the tools and parameters that were used to process and annotate this data. These guidelines must address a broad range of issues, as glycomics data are inherently complex and are generated using diverse methods, including mass spectrometry (MS), chromatography, glycan array-binding assays, nuclear magnetic resonance (NMR) and other rapidly developing technologies. The acceptance of these guidelines by scientists conducting research on biological systems in which glycans have a significant role will facilitate the evaluation and reproduction of glycomics experiments and data that is reported in scientific journals and uploaded to glycomics databases. As a first step, MIRAGE guidelines for glycan analysis by MS have been recently published (Kolarich D, Rapp E, Struwe WB, Haslam SM, Zaia J., et al. 2013. The minimum information required for a glycomics experiment (MIRAGE) project - Improving the standards for reporting mass spectrometry-based glycoanalytic data. Mol. Cell Proteomics. 12:991-995), allowing them to be implemented and evaluated in the context of real-world glycobiology research. In this paper, we set out the historical context, organization structure and overarching objectives of the MIRAGE initiative.
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| 3. |
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| 6. |
- Gupta, Kallol, et al.
(författare)
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The role of interfacial lipids in stabilizing membrane protein oligomers
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 541:7637, s. 421-424
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Tidskriftsartikel (refereegranskat)abstract
- Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways(1) but is often difficult to define(2) or predict(3). Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 alpha-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability. For the bacterial homologue of the eukaryotic biogenic transporters (LeuT(4), one of the proteins with the lowest oligomeric stability), we found a precise cohort of lipids within the dimer interface. Delipidation, mutation of lipid-binding sites or expression in cardiolipin-deficient Escherichia coli abrogated dimer formation. Molecular dynamics simulation revealed that cardiolipin acts as a bidentate ligand, bridging across subunits. Subsequently, we show that for the Vibrio splendidus sugar transporter SemiSWEET(5), another protein with low oligomeric stability, cardiolipin shifts the equilibrium from monomer to functional dimer. We hypothesized that lipids are essential for dimerization of the Na+/H+ antiporter NhaA from E. coli, which has the lowest oligomeric strength, but not for the substantially more stable homologous Thermus thermophilus protein NapA. We found that lipid binding is obligatory for dimerization of NhaA, whereas NapA has adapted to form an interface that is stable without lipids. Overall, by correlating interfacial strength with the presence of interfacial lipids, we provide a rationale for understanding the role of lipids in both transient and stable interactions within a range of a-helical membrane proteins, including G-protein-coupled receptors.
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| 7. |
- Miller, R. L., et al.
(författare)
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Shotgun ion mobility mass spectrometry sequencing of heparan sulfate saccharides
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Despite evident regulatory roles of heparan sulfate (HS) saccharides in numerous biological processes, definitive information on the bioactive sequences of these polymers is lacking, with only a handful of natural structures sequenced to date. Here, we develop a "Shotgun" Ion Mobility Mass Spectrometry Sequencing (SIMMS2) method in which intact HS saccharides are dissociated in an ion mobility mass spectrometer and collision cross section values of fragments measured. Matching of data for intact and fragment ions against known values for 36 fully defined HS saccharide structures (from di- to decasaccharides) permits unambiguous sequence determination of validated standards and unknown natural saccharides, notably including variants with 3O-sulfate groups. SIMMS2 analysis of two fibroblast growth factor-inhibiting hexasaccharides identified from a HS oligosaccharide library screen demonstrates that the approach allows elucidation of structure-activity relationships. SIMMS2 thus overcomes the bottleneck for decoding the informational content of functional HS motifs which is crucial for their future biomedical exploitation. Heparan sulfates (HS) contain functionally relevant structural motifs, but determining their monosaccharide sequence remains challenging. Here, the authors develop an ion mobility mass spectrometry-based method that allows unambiguous characterization of HS sequences and structure-activity relationships.
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| 8. |
- Mölstad, S., et al.
(författare)
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Strama-a Swedish working model for containment of antibiotic resistance.
- 2008
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Ingår i: Euro surveillance : bulletin européen sur les maladies transmissibles = European communicable disease bulletin. - 1025-496X. ; 13:46
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Tidskriftsartikel (refereegranskat)abstract
- The overall aim of Strama (The Swedish Strategic Programme Against Antibiotic Resistance) is to preserve the effectiveness of antibiotics in humans and animals. Strama is organised at two levels: a network of independent local multidis ciplinary groups in each county that provide prescribers with feedback on antibiotic use and resistance and implement guidelines; and a national executive working group funded by the government. To gain an insight into antibiotic use, Strama has conducted several large diagnosis prescribing surveys in primary care, in the hospital settings and in nursing homes. National antibiotic susceptibility data for Sweden and mandatory notification show that in recent years the proportion of Streptococcus pneumoniae with decreased sensitivity to penicillin V has stabilised (around 6 %), but the number of notified cases of meticillin-resistant Staphylococcus aureus (MRSA)has increased and ESBL-producing Enterobacteraceae have turned into an endemic situation. Still, Sweden is among the countries with the lowest rates of MRSA (<1 %), S. pneumoniae can still be treated with penicillin V and the rate of Escherichia coli-producingESBLs is below 5 %. Strama's activities have contributed to a steady decrease in antibiotic use from the mid 1990s until 2004(when total use slowly started to increase again) without measurable negative consequences. Regular collaboration with national and regional news media has been one of the key strategies.
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| 9. |
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| 10. |
- Rojas-Macias, Miguel A., 1979, et al.
(författare)
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Towards a standardized bioinformatics infrastructure for N- and O-glycomics
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N-and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.
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| 11. |
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| 12. |
- Struwe, Henry, et al.
(författare)
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Telescoping a Prenyltransferase and a Diterpene Synthase to Transform Unnatural FPP Derivatives to Diterpenoids
- 2024
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 26:28, s. 5888-5892
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Tidskriftsartikel (refereegranskat)abstract
- New diterpenoids are accessible from non-natural FPP derivatives as substrates for an enzymatic elongation cyclization cascade using the geranylgeranyl pyrophosphate synthase (GGPPS) from Streptomyces cyaneofuscatus and the spata-13,17-diene synthase (SpS) from Streptomyces xinghaiensis. This approach led to four new biotransformation products including three new cyclododecane cores and a macrocyclic ether. For the first time, a 1,12-terpene cyclization was observed when shifting the central olefinic double bond toward the geminial methyl groups creating a nonconjugated 1,4-diene.
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| 13. |
- Struwe, Lena, 1967-
(författare)
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Morphological and Molecular Phylogenetic Studies in Neotropical Gentianaceae
- 1999
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The Gentianaceae of the Neotropics are a diverse taxonomic group representing several evolutionary lineages. The phylogenetic relationships of neotropical gentians are discussed based on cladistic analyses of morphological, trnL intron, and ITS 1 sequence data. Support for specific morphological and anatomical character evolutionary and biogeographic hypotheses are evaluated, with an emphasis on taxa from the Guayana Shield.Saccifolium, the only member of the family Saccifoliaceae, was found to be closely related to Gentiana and associated temperate-alpine genera. The boreotropics hypothesis is suggested as an explanation for the isolated occurrence of Saccifolium on the tepui complex Sierra de la Neblina (Brazilian-Venezuelan border), far from possible close relatives in eastern North America. Saccifolium is now considered a member of Gentianaceae due to this result.The majority of neotropical gentians belong to the Helia clade, a monophyletic, natural group restricted to the Neotropics. The Helia clade shows great morphological variation and occur in a diversity of habitats and geographic areas. Secondary woodiness appears to have evolved independently in this clade and in the Potalia clade, with perennial herbs being ancestral. Floral characters are also discussed from a phylogenetic perspective. The Helia clade has a high rate of white-sand and tepui endemic species including some that have been recently described. Several white-sand species are suggested to be relicts of basal evolutionary lineages in the tribe. The Pantepui and Quaternary forest refugium theory is discussed, and preliminary data suggest several independent origins of highland taxa from lowland lineages.The genus Potalia is most closely related to the African and Malagasy genus Anthocleista and it is suggested that the boreotropics hypothesis also explains their distribution. The first monograph of Potalia is presented. Potalia amara, the type species, is restricted to French Guiana and Amapá, Brazil. Three additional species are restricted to white-sand areas in lowlands of Amazonia and the Guayana Shield, and two species are restricted to Chocó, Colombia, and Panama and Costa Rica, respectively. Potalia resinifera is the most widespread species occurring over most of the Amazon basin, Andean foothills, and the Chocó. A morphological cladistic analysis of Potalia is presented, and this supports the proposed theory of white-sand taxa being representatives of basal, relictual lineages in neotropical plant groups (as in the Helia clade).<>P A cladistic analysis of the mycotrophic genus Voyria based on morphology and anatomy resulted in two large, monophyletic lineages, identified as two new subgenera. Ancestral distributions of Voyria and Potalia on the Guayana Shield are supported by morphological cladistic studies.
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| 14. |
- Struwe, W. B., et al.
(författare)
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Identification of O-glycan Structures from Chicken Intestinal Mucins Provides Insight into Campylobactor jejuni Pathogenicity
- 2015
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476. ; 14:6, s. 1464-1477
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Tidskriftsartikel (refereegranskat)abstract
- The Gram-negative bacteria Campylobactor jejuni is the primary bacteria responsible for food poisoning in industrialized countries, and acute diarrheal illness is a leading cause of mortality among children in developing countries. C. jejuni are commensal in chickens. They are particularly abundant in the caecal crypts, and poultry products are commonly infected as a result of cross-contamination during processing. The interactions between C. jejuni and chicken intestinal tissues as well as the pathogenic molecular mechanisms of colonization in humans are unknown, but identifying these factors could provide potential targets to reduce the incidence of campylobacteriosis. Recently, purified chicken intestinal mucin was shown to attenuate adherence and invasion of C. jejuni in the human colorectal adenocarcinoma cell line HCT-8 in vitro, and this effect was attributed to mucin O-glycosylation. Mucins from different regions of the chicken intestine inhibited C. jejuni binding and internalization differentially, with large intestine>small intestine>caecum. Here, we use LC-MS to perform a detailed structural analysis of O-glycans released from mucins purified from chicken large intestine, small intestine, and caecum. The O-glycans identified were abundantly sulfated compared with the human intestines, and sulfate moieties were present throughout the chicken intestinal tract. Interestingly, alpha 1-2 linked fucose residues, which have a high binding affinity to C. jejuni, were identified in the small and large intestines. Additionally, N-glycolylneuraminic/N-acetylneuraminic acid containing structures present as Sda-like epitopes were identified in large intestine samples but not small intestine or caecum. O-glycan structural characterization of chicken intestinal mucins provides insights into adherence and invasion properties of C. jejuni, and may offer prospective candidate molecules aimed at reducing the incidence of infection.
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| 15. |
- Struwe, Weston B, et al.
(författare)
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The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets.
- 2016
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 1460-2423 .- 0959-6658. ; 26:9, s. 907-910
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Tidskriftsartikel (refereegranskat)abstract
- Theminimum information required for a glycomics experiment (MIRAGE) project was established in 2011 to provide guidelines to aid in data reporting from all types of experiments in glycomics research including mass spectrometry (MS), liquid chromatography, glycan arrays, data handling and sample preparation. MIRAGE is a concerted effort of the wider glycomics community that considers the adaptation of reporting guidelines as an important step towards critical evaluation and dissemination of datasets as well as broadening of experimental techniques worldwide. The MIRAGE Commission published reporting guidelines for MS data and here we outline guidelines for sample preparation. The sample preparation guidelines include all aspects of sample generation, purification and modification from biological and/or synthetic carbohydrate material. The application of MIRAGE sample preparation guidelines will lead to improved recording of experimental protocols and reporting of understandable and reproducible glycomics datasets.
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