Publications
27 results found
Ribeiro DO, Pinheiro BA, Bras JLA, et al., 2022, Protein-carbohydrate recognition in the biodegradation of plant cell wall: functional studies using carbohydrate microarrays, Publisher: WILEY, Pages: 46-46, ISSN: 2211-5463
Akune Y, Arpinar S, Silva LM, et al., 2022, CarbArrayART-An update on the software tool for carbohydrate microarray data, storage, processing, presentation and reporting, Glycobiology, Vol: 30, Pages: 1031-1031, ISSN: 0959-6658
Glycan microarrays are essential tools in glycobiology and are being widely used for assignment of glycan ligands in diverse glycan recognition systems. We have developed a new software, called Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART), to address the need for a distributable application for glycan microarray data management. The main features of CarbArrayART include: (i) Storage of quantified array data from different array layouts with scan data and array-specific metadata, such as lists of arrayed glycans, array geometry, information on glycan-binding samples, and experimental protocols. (ii) Presentation of microarray data as charts, tables, and heatmaps derived from the average fluorescence intensity values that are calculated based on the imaging scan data and array geometry, as well as filtering and sorting functions according to monosaccharide content and glycan sequences. (iii) Data export for reporting in Word, PDF, and Excel formats, together with metadata that are compliant with the guidelines of MIRAGE (Minimum Information Required for A Glycomics Experiment). CarbArrayART is designed for routine use in recording, storage, and management of any slide-based glycan microarray experiment. In conjunction with the MIRAGE guidelines, CarbArrayART addresses issues that are critical for glycobiology, namely, clarity of data for evaluation of reproducibility and validity.
Correia VG, Trovao F, Pinheiro BA, et al., 2021, Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont <i>Bacteroides ovatus</i>, MICROBIOLOGY SPECTRUM, Vol: 9, ISSN: 2165-0497
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- Citations: 3
McAllister N, Liu Y, Silva LM, et al., 2021, Chikungunya Virus Strains from Each Genetic Clade Bind Sulfated Glycosaminoglycans as Attachment Factors (vol 94, e01500-20, 2020), JOURNAL OF VIROLOGY, Vol: 95, ISSN: 0022-538X
Chai W, Li C, Palma A, et al., 2021, Noncovalent microarrays from synthetic amino-terminating glycans: Implications in expanding glycan microarray diversity and platform comparison, Glycobiology, Vol: 31, Pages: 931-946, ISSN: 0959-6658
Glycan microarrays have played important roles in detection and specificity assignment of glycan recognition by proteins. However, the size and diversity of glycan libraries in current microarray systems are small compared to estimated glycomes, and these may lead to missed detection or incomplete assignment. For microarray construction, covalent and noncovalent immobilization are the two types of methods used, but a direct comparison of results from the two platforms is required. Here we develop a chemical strategy to prepare lipid-linked probes from both naturally derived aldehyde-terminating and synthetic amino-terminating glycans that addresses the two aspects: expansion of sequence-defined glycan libraries and comparison of the two platforms. We demonstrate the specific recognition by plant and mammalian lectins, carbohydrate-binding modules and antibodies and the overall similarities from the two platforms. Our results provide new knowledge on unique glycan-binding specificities for the immune receptor Dectin-1 toward β-glucans and the interaction of rotavirus P[19] adhesive protein with mucin O-glycan cores.
Silva LM, Correia VG, Moreira ASP, et al., 2021, Helicobacter pylori lipopolysaccharide structural domains and their recognition by immune proteins revealed with carbohydrate microarrays, Carbohydrate Polymers, Vol: 253, ISSN: 0144-8617
The structural diversity of the lipopolysaccharides (LPSs) from Helicobacter pylori poses a challenge to establish accurate and strain-specific structure-function relationships in interactions with the host. Here, LPS structural domains from five clinical isolates were obtained and compared with the reference strain 26695. This was achieved combining information from structural analysis (GC-MS and ESI-MSn) with binding data after interrogation of a LPS-derived carbohydrate microarray with sequence-specific proteins. All LPSs expressed Lewisx/y and N-acetyllactosamine determinants. Ribans were also detected in LPSs from all clinical isolates, allowing their distinction from the 26695 LPS. There was evidence for 1,3-d-galactans and blood group H-type 2 sequences in two of the clinical isolates, the latter not yet described for H. pylori LPS. Furthermore, carbohydrate microarray analyses showed a strain-associated LPS recognition by the immune lectins DC-SIGN and galectin-3 and revealed distinctive LPS binding patterns by IgG antibodies in the serum from H. pylori-infected patients.
McAllister N, Liu Y, Silva LM, et al., 2020, Chikungunya virus strains from each genetic clade bind sulfated glycosaminoglycans as attachment factors, Journal of Virology, Vol: 94, ISSN: 0022-538X
Chikungunya virus (CHIKV) is an arthritogenic alphavirus that causes debilitating musculoskeletal disease. CHIKV displays broad cell, tissue, and species tropism, which may correlate with the attachment factors and entry receptors used by the virus. Cell-surface glycosaminoglycans (GAGs) have been identified as CHIKV attachment factors. However, the specific types of GAGs and potentially other glycans to which CHIKV binds and whether there are strain-specific differences in GAG binding is not fully understood. To identify the types of glycans bound by CHIKV, we conducted glycan microarray analyses and discovered that CHIKV preferentially binds GAGs. Microarray results also indicate that sulfate groups on GAGs are essential for CHIKV binding and that CHIKV binds most strongly to longer GAG chains of heparin and heparan sulfate. To determine whether GAG-binding capacity varies among CHIKV strains, a representative strain from each genetic clade was tested. While all strains directly bound to heparin and chondroitin sulfate in ELISAs and depended on heparan sulfate for efficient cell-binding and infection, we observed some variation by strain. Enzymatic removal of cell-surface GAGs and genetic ablation that diminishes GAG expression reduced CHIKV binding and infectivity of all strains. Collectively, these data demonstrate that GAGs are the preferred glycan bound by CHIKV, enhance our understanding of the specific GAG moieties required for CHIKV binding, define strain differences in GAG engagement, and provide further evidence for a critical function of GAGs in CHIKV cell attachment and infection.IMPORTANCE Alphavirus infections are a global health threat, contributing to outbreaks of disease in many parts of the world. Recent epidemics caused by CHIKV, an arthritogenic alphavirus, resulted in more than 8.5 million cases as the virus has spread into new geographic regions, including the Western Hemisphere. CHIKV causes disease in the majority of people infected, leading
Ribeiro DO, Costa R, Pinheiro BA, et al., 2020, Unravelling Clostridium thermocellum LysM domains: Structural basis for the recognition of chitin and peptidoglycan, Publisher: OXFORD UNIV PRESS INC, Pages: 1099-1100, ISSN: 0959-6658
Vendele I, Willment JA, Silva LM, et al., 2020, Mannan detecting C-type lectin receptor probes recognise immune epitopes with diverse chemical, spatial and phylogenetic heterogeneity in fungal cell walls, PLoS Pathogens, Vol: 16, Pages: 1-29, ISSN: 1553-7366
During the course of fungal infection, pathogen recognition by the innate immune system is critical to initiate efficient protective immune responses. The primary event that triggers immune responses is the binding of Pattern Recognition Receptors (PRRs), which are expressed at the surface of host immune cells, to Pathogen-Associated Molecular Patterns (PAMPs) located predominantly in the fungal cell wall. Most fungi have mannosylated PAMPs in their cell walls and these are recognized by a range of C-type lectin receptors (CTLs). However, the precise spatial distribution of the ligands that induce immune responses within the cell walls of fungi are not well defined. We used recombinant IgG Fc-CTLs fusions of three murine mannan detecting CTLs, including dectin-2, the mannose receptor (MR) carbohydrate recognition domains (CRDs) 4–7 (CRD4-7), and human DC-SIGN (hDC-SIGN) and of the β-1,3 glucan-binding lectin dectin-1 to map PRR ligands in the fungal cell wall of fungi grown in vitro in rich and minimal media. We show that epitopes of mannan-specific CTL receptors can be clustered or diffuse, superficial or buried in the inner cell wall. We demonstrate that PRR ligands do not correlate well with phylogenetic relationships between fungi, and that Fc-lectin binding discriminated between mannosides expressed on different cell morphologies of the same fungus. We also demonstrate CTL epitope differentiation during different phases of the growth cycle of Candida albicans and that MR and DC-SIGN labelled outer chain N-mannans whilst dectin-2 labelled core N-mannans displayed deeper in the cell wall. These immune receptor maps of fungal walls of in vitro grown cells therefore reveal remarkable spatial, temporal and chemical diversity, indicating that the triggering of immune recognition events originates from multiple physical origins at the fungal cell surface.
Wu N, Silva LM, Liu Y, et al., 2019, Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays., Mol Cell Proteomics, Vol: 18, Pages: 1981-2002, ISSN: 1535-9476
Glycan antigens recognized by monoclonal antibodies have served as stem cell markers. To understand regulation of their biosynthesis and their roles in stem cell behavior precise assignments are required. We have applied state-of-the-art glycan array technologies to compare the glycans bound by five antibodies that recognize carbohydrates on human stem cells. These are: FC10.2, TRA-1-60, TRA-1-81, anti-i and R-10G. Microarray analyses with a panel of sequence-defined glycans corroborate that FC10.2, TRA-1-60, TRA-1-81 recognize the type 1-(Galβ-3GlcNAc)-terminating backbone sequence, Galβ-3GlcNAcβ-3Galβ-4GlcNAcβ-3Galβ-4GlcNAc, and anti-i, the type 2-(Galβ-4GlcNAc) analog, Galβ-4GlcNAcβ-3Galβ-4GlcNAcβ-3Galβ-4GlcNAc, and we determine substituents they can accommodate. They differ from R-10G, which requires sulfate. By Beam Search approach, starting with an antigen-positive keratan sulfate polysaccharide, followed by targeted iterative microarray analyses of glycan populations released with keratanases and mass spectrometric monitoring, R-10G is assigned as a mono-sulfated type 2 chain with 6-sulfation at the penultimate N-acetylglucosamine, Galβ-4GlcNAc(6S)β-3Galβ-4GlcNAcβ-3Galβ-4GlcNAc. Microarray analyses using newly synthesized glycans corroborate the assignment of this unique determinant raising questions regarding involvement as a ligand in the stem cell niche.
Chandra N, Liu Y, Liu J-X, et al., 2019, Sulfated glycosaminoglycans as viral decoy receptors for human adenovirus type 37, Viruses, Vol: 11, ISSN: 1999-4915
Glycans on plasma membranes and in secretions play important roles in infection by many viruses. Species D human adenovirus type 37 (HAdV-D37) is a major cause of epidemic keratoconjunctivitis (EKC) and infects target cells by interacting with sialic acid (SA)-containing glycans via the fiber knob domain of the viral fiber protein. HAdV-D37 also interacts with sulfated glycosaminoglycans (GAGs), but the outcome of this interaction remains unknown. Here, we investigated the molecular requirements of HAdV-D37 fiber knob:GAG interactions using a GAG microarray and demonstrated that fiber knob interacts with a broad range of sulfated GAGs. These interactions were corroborated in cell-based assays and by surface plasmon resonance analysis. Removal of heparan sulfate (HS) and sulfate groups from human corneal epithelial (HCE) cells by heparinase III and sodium chlorate treatments, respectively, reduced HAdV-D37 binding to cells. Remarkably, removal of HS by heparinase III enhanced the virus infection. Our results suggest that interaction of HAdV-D37 with sulfated GAGs in secretions and on plasma membranes prevents/delays the virus binding to SA-containing receptors and inhibits subsequent infection. We also found abundant HS in the basement membrane of the human corneal epithelium, which may act as a barrier to sub-epithelial infection. Collectively, our findings provide novel insights into the role of GAGs as viral decoy receptors and highlight the therapeutic potential of GAGs and/or GAG-mimetics in HAdV-D37 infection.
Rudkin FM, Raziunaite I, Workman H, et al., 2019, Single human B cell-derived monoclonal anti-<i>Candida</i> antibodies enhance phagocytosis and protect against disseminated candidiasis (vol 9, 5288, 2018), NATURE COMMUNICATIONS, Vol: 10, ISSN: 2041-1723
Rudkin FM, Raziunaite I, Workman H, et al., 2018, Single human B cell-derived monoclonal anti-<i>Candida</i> antibodies enhance phagocytosis and protect against disseminated candidiasis, NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723
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- Citations: 43
Akune Y, Arpinar S, Silva LM, et al., 2018, CarbArrayART: Carbohydrate Array Analysis and Reporting Tool New software for glycan array for data processing, storage and presentation, Annual Meeting of the Society-for-Glycobiology (SFG), Publisher: OXFORD UNIV PRESS INC, Pages: 1034-1035, ISSN: 0959-6658
Loureiro LR, Sousa DP, Ferreira D, et al., 2018, Novel monoclonal antibody L2A5 specifically targeting sialyl-Tn and short glycans terminated by alpha-2–6 sialic acids, Scientific Reports, Vol: 8, ISSN: 2045-2322
Incomplete O-glycosylation is a feature associated with malignancy resulting in the expression of truncated glycans such as the sialyl-Tn (STn) antigen. Despite all the progress in the development of potential anti-cancer antibodies, their application is frequently hindered by low specificities and cross-reactivity. In this study, a novel anti-STn monoclonal antibody named L2A5 was developed by hybridoma technology. Flow cytometry analysis showed that L2A5 specifically binds to sialylated structures on the cell surface of STn-expressing breast and bladder cancer cell lines. Moreover, immunoblotting assays demonstrated reactivity to tumour-associated O-glycosylated proteins, such as MUC1. Tumour recognition was further observed using immunohistochemistry assays, which demonstrated a high sensitivity and specificity of L2A5 mAb towards cancer tissue, using bladder and colorectal cancer tissues. L2A5 staining was exclusively tumoural, with a remarkable reactivity in invasive and metastasis sites, not detectable by other anti-STn mAbs. Additionally, it stained 20% of cases of triple-negative breast cancers, suggesting application in diseases with unmet clinical needs. Finally, the fine specificity was assessed using glycan microarrays, demonstrating a highly specific binding of L2A5 to core STn antigens and additional ability to bind 2–6-linked sialyl core-1 probes. In conclusion, this study describes a novel anti-STn antibody with a unique binding specificity that can be applied for cancer diagnostic and future development of new antibody-based therapeutic applications.
Akune Y, Arpinar S, Stoll M, et al., 2017, New software for glycan array for data processing, storage and presentation, Annual Meeting of the Society-for-Glycobiology, Publisher: OXFORD UNIV PRESS INC, Pages: 1204-1204, ISSN: 0959-6658
Li Z, Gao C, Zhang Y, et al., 2017, O-Glycome beam search arrays for carbohydrate ligand discovery, Molecular and Cellular Proteomics, Vol: 17, Pages: 121-133, ISSN: 1535-9476
O-glycosylation is a post-translational modification of proteins crucial to molecular mechanisms in health and disease. O-glycans are typically highly heterogeneous. The involvement of specific O-glycan sequences in many bio-recognition systems is yet to be determined due to a lack of efficient methodologies. We describe here a targeted microarray approach: O-glycome beam search that is both robust and efficient for O-glycan ligand-discovery. Substantial simplification of the complex O-glycome profile and facile chromatographic resolution is achieved by arraying O-glycans as branches, monitoring by mass spectrometry, focusing on promising fractions, and on-array immuno-sequencing. This is orders of magnitude more sensitive than traditional methods. We have applied beam search approach to porcine stomach mucin and identified extremely minor components previously undetected within the O-glycome of this mucin that are ligands for the adhesive proteins of two rotaviruses. The approach is applicable to O-glycome recognition studies in a wide range of biological settings to give insights into glycan recognition structures in natural microenvironments.
Liu Y, McBride R, Stoll M, et al., 2016, The Minimum Information Required for a Glycomics Experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data, Glycobiology, Vol: 27, Pages: 280-284, ISSN: 1460-2423
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 (MS) 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.
Correia VG, Bras JLA, Liu Y, et al., 2016, An integrative strategy to decipher glycan recognition in the human gut microbiome, Annual Meeting of the Society-for-Glycobiology, Publisher: OXFORD UNIV PRESS INC, Pages: 1398-1399, ISSN: 0959-6658
Silva L, Childs RA, Palma AS, et al., 2015, Influence of carrier lipid composition on glycan recognition in NGL-based microarrays, Annual Meeting of the Society-for-Glycobiology on Glycobiology - Accelerating Impact across the Biomedical Sciences, Publisher: OXFORD UNIV PRESS INC, Pages: 1260-1260, ISSN: 0959-6658
Silva L, 2014, Structural analysis of glycans and development of microarrays from Helicobacter pylori cell surface glycome
Silva L, Shahidi F, Coimbra MA, 2012, Dried Pears: Phytochemicals and Potential Health Effects, Dried Fruits Phytochemicals and Health Effects, Editors: Alasalvar, Shahidi, Publisher: John Wiley & Sons, Pages: 325-356, ISBN: 9781118464649
Contributors to this volume are internationally renowned researchers who have provided a comprehensive account of the global perspectives of the issues relating to phytochemicals and health effects of dried fruits.
Nunes C, Silva L, Fernandes AP, et al., 2012, Occurrence of cellobiose residues directly linked to galacturonic acid in pectic polysaccharides, CARBOHYDRATE POLYMERS, Vol: 87, Pages: 620-626, ISSN: 0144-8617
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- Citations: 50
Ferreira JA, Silva L, Monteiro MA, et al., 2011, Helicobacter pylori cell-surface glycans structural features: role in gastric colonization, pathogenesis, and carbohydrate-based vaccines, Carbohydrate Chemistry, Editors: Rauter, Lindhorst, Publisher: Royal Society of Chemistry, Pages: 160-193, ISBN: 9781849731546
Each volume of the series brings together references to all published work in given areas of the subject and serves as a comprehensive database for the active research chemist Specialist Periodical Reports provide systematic and detailed ...
Silva L, Garcia B, Paiva-Martins F, 2010, Oxidative stability of olive oil and its polyphenolic compounds after boiling vegetable process, LWT - Food Science and Technology, Vol: 43, Pages: 1336-1344, ISSN: 0023-6438
Silva L, Pinto J, Carrola J, et al., 2010, Oxidative stability of olive oil after food processing and comparison with other vegetable oils, Food Chemistry, Vol: 121, Pages: 1177-1187, ISSN: 0308-8146
Paiva-Martins F, Fernandes J, Santos V, et al., 2010, Powerful protective role of 3,4-dihydroxyphenylethanol-elenolic acid dialdehyde against erythrocyte oxidative-induced hemolysis., J Agric Food Chem, Vol: 58, Pages: 135-140
The present work studied and compared the capacity of four important olive oil polyphenolic compounds, oleuropein, hydroxytyrosol, and the oleuropein aglycones 3,4-dihydroxyphenylethanol-elenolic acid (3,4-DHPEA-EA) and 3,4-dihydroxyphenylethanol-elenolic acid dialdehyde (3,4-DHPEA-EDA), to protect red blood cells (RBCs) from oxidative hemolysis induced by the physiological initiator H2O2. The amount of hemolysis was evaluated spectrophotometrically. The compounds were also tested in the presence and absence of the naturally occurring antioxidant ascorbic acid. All compounds were revealed to significantly protect RBCs from oxidative hemolysis induced by H2O2 at 40 and 80 microM, with the order of activity being 3,4-DHPEA-EDA>3,4-DHPEA-EA>hydroxytyrosol=oleuropein. At 20, 10, and 5 microM, only 3,4-DHPEA-EDA showed a significant protection against the oxidative injury. In the presence of ascorbic acid at physiological concentration, the addition of individual compounds at 40 microM increased the stability of erythrocytes. The addition of phenolic compounds at 20 and 10 microM did not produce further protection when compared with the protection given by ascorbic acid alone, except for 3,4-DHPEA-EDA. This compound was shown to produce further protection even at 5 microM. In summary, 3,4-DHPEA-EDA plays an important protective role against reactive oxygen species-induced oxidative injury in RBCs, and this effect is more potent than the one evidenced by hydroxytyrosol or oleuropein.
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