A5075340620- Glycosylation and Glycoproteins Research
- Monoclonal and Polyclonal Antibodies Research
- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Carbohydrate Chemistry and Synthesis
- Galectins and Cancer Biology
- Infections and bacterial resistance
- Cystic Fibrosis Research Advances
- SARS-CoV-2 and COVID-19 Research
- Bacterial biofilms and quorum sensing
- Viral Infectious Diseases and Gene Expression in Insects
- Transgenic Plants and Applications
- Microfluidic and Capillary Electrophoresis Applications
- Cell Adhesion Molecules Research
- Legionella and Acanthamoeba research
- Pneumonia and Respiratory Infections
- Bacterial Infections and Vaccines
- Urticaria and Related Conditions
- Trace Elements in Health
- Bacillus and Francisella bacterial research
- Autoimmune Bullous Skin Diseases
- Vibrio bacteria research studies
- Microbial Inactivation Methods
- Scientific Computing and Data Management
VIB-UGent Center for Medical Biotechnology
2020-2025
Ghent University
2014-2025
Ghent University Hospital
2025
Various adverse cutaneous reactions to anti-TNF-α monoclonal antibody have been reported. In clinical studies with infliximab (Remicade<sup>®</sup>) drug were most frequently reported in the respiratory system and skin appendages. We describe here 6 patients receiving anti- TNF-α therapy (infliximab) for Crohn’s disease or rheumatoid arthritis who consulted our out-patient department between November 1999 February 2002. The following diagnoses made: leukocytoclastic vasculitis,...
Outer membrane vesicles (OMVs) are small nanoscale structures that secreted by bacteria and can carry nucleic acids, proteins, metabolites. They mediate intracellular communication play a role in virulence. In this study, we show treatment with the β-lactam antibiotic imipenem leads to dramatic increase secretion of outer nosocomial pathogen Stenotrophomonas maltophilia. Proteomic analysis their protein content demonstrated OMVs contain chromosomal encoded L1 metallo-β-lactamase L2...
Several bacterial species produce membrane vesicles (MVs) in response to antibiotic stress. However, the biogenesis and role of MVs resistance mechanisms have remained unclear. Here, we studied effect fluoroquinolone ciprofloxacin on MV secretion by Stenotrophomonas maltophilia using a combination electron microscopy proteomic approaches. We found that addition classical outer (OMV), ciprofloxacin-stimulated cultures produced larger containing both inner membranes termed outer-inner (OIMV),...
Broadly neutralizing antibodies are an important treatment for individuals with coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome 2 (SARS-CoV-2). Antibody-based therapeutics also essential pandemic preparedness against future Sarbecovirus outbreaks. Camelid-derived single domain (VHHs) exhibit potent antimicrobial activity and being developed as SARS-CoV-2–neutralizing antibody-like therapeutics. Here, we identified VHHs that neutralize both SARS-CoV-1...
Data-independent acquisition (DIA) has become a well-established method for MS-based proteomics. However, the list of options to analyze this type data is quite extensive, and use spectral libraries an important factor in DIA analysis. More specifically silico predicted gaining more interest. By working with differential spike-in human standard proteins (UPS2) constant yeast tryptic digest background, we evaluated sensitivity, precision, accuracy analysis workflows compared established...
Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated mass spectrometry-based proteomics laboratories. However, lack standardized quality practices across laboratories poses challenges for comparability reproducibility. In response, we conducted harmonization study within Core Life alliance with aim establishing common framework, which facilitates comprehensive assessment identification potential sources performance drift. Through...
Abstract Background Fecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. metaproteomics provides valuable insights by tracking changes the relative abundance of microbial taxa their protein functions. To ensure reliable results, it is crucial to minimize alterations metaproteome occurring from sample collection extraction. Therefore, employing effective stabilization methods essential preserve integrity fecal laboratory analysis,...
The treatment ofStenotrophomonas maltophiliainfection with β-lactam antibiotics leads to increased release of outer membrane vesicles (OMVs), which are packed two chromosomally encoded β-lactamases. Here, we show that these β-lactamase-packed OMVs capable establishing extracellular degradation. We also they dramatically increase the apparent MICs imipenem and ticarcillin for cohabituating speciesPseudomonas aeruginosaandBurkholderia cenocepacia.
As small and stable high-affinity antigen binders, VHHs boast attractive characteristics both for therapeutic use in various disease indications, as versatile reagents research diagnostics. To further increase the versatility of VHHs, we explored VHH scaffold a structure-guided approach to select regions where introduction an N-glycosylation N-X-T sequon its associated glycan should not interfere with protein folding or epitope recognition. We expressed variants such glycoengineered Pichia...
Abstract The glycosylation pathways of several eukaryotic protein expression hosts are being engineered to enable the production therapeutic glycoproteins with humanized application‐customized glycan structures. In hosts, this has been quite successful, but one caveat is that new N ‐glycan structures inadvertently might be substrates for or more multitude endogenous glycosyltransferases in such heterologous background. This then results formation novel, undesired structures, which often...
Maackia amurensis lectins serve as research and botanical agents that bind to sialic residues on proteins. For example, M. seed lectin (MASL) targets the acid modified podoplanin (PDPN) receptor suppress arthritic chondrocyte inflammation, inhibit tumor cell growth motility. However, nomenclature composition are not clearly defined. Here, we sought definitively characterize MASL its effects behavior. We utilized SDS-PAGE LC-MS/MS find can be divided into two groups. is a member of one group...
With current trends in proteomics, especially regarding clinical and low input (to single cell) samples, it is increasingly important to both maximize the throughput of analysis maintain as much sensitivity possible. The new generation mass spectrometers (MS) are taking a huge leap sensitivity, allowing samples with shorter liquid chromatography (LC) methods while digging deep proteome. However, can be doubled by implementing dual column nano-LC-MS configuration. For this purpose, we used...
Abstract Currently circulating SARS-CoV-2 variants have gained complete or significant resistance to all SARS-CoV-2-neutralizing antibodies that been used in the clinic. Such can prevent severe disease exposed patients for whom vaccines may not provide optimal protection. Here, we describe single-domain (VHHs), also known as nanobodies, broadly neutralize with unusually high potency. Structural analysis revealed their binding a unique, highly conserved, membrane proximal, quaternary epitope...
Abstract We have identified camelid single-domain antibodies (VHHs) that cross-neutralize SARS-CoV-1 and −2, such as VHH72, which binds to a unique highly conserved epitope in the viral receptor-binding domain (RBD) is difficult access for human antibodies. Here, we establish protein engineering path how stable, long-acting drug candidate can be generated out of VHH building block. When fused IgG1-Fc, prototype VHH72 molecule prophylactically protects hamsters from SARS-CoV-2. In addition,...
Abstract Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still lot of possibilities at the data analysis level. By benchmarking different DIA workflows using ground-truth sample, consisting differential spike-in UPS2 constant yeast background, we provide roadmap for shotgun samples based on whether sensitivity, precision or accuracy is essence. Three commonly used software tools (DIA-NN, EncyclopeDIA and Spectronaut...
ABSTRACT With current trends in proteomics, especially regarding clinical and low input (to single cell) samples, it is increasingly important to both maximize the throughput of analysis maintain as much sensitivity possible. The new generation mass spectrometers (MS) are taking a huge leap sensitivity, allowing analyze samples with shorter liquid chromatography (LC) methods while digging deep proteome. However, can be doubled by implementing dual column nano-LC-MS configuration. For this...
Abstract Monoclonal antibodies are the leading drug of biopharmaceutical market because their high specificity and tolerability, but current CHO-based manufacturing platform remains expensive time-consuming to limited accessibility, especially in case diseases with incidence pandemics. Therefore, there is an urgent need for alternative production system. In this study, we present a rapid cost-effective microbial heavy chain-only (VHH-Fc) methylotrophic yeast Komagataella phaffii (aka Pichia...
Abstract Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated mass spectrometry-based proteomics laboratories. However, lack standardized quality practices across laboratories poses challenges for comparability reproducibility. In response, we conducted harmonization study within Core Life alliance with aim to establish common framework, which facilitates comprehensive assessment identification potential sources performance drift....
Proteins organize into functional assemblies that drive diverse biological activities. Leveraging a comprehensive dataset of manually curated annotations for the human protein complexome, we investigated perturbations at complex level. Using proteomics and transcriptomics data from fibroblasts patients with inborn errors metabolism (IEM) control samples, globally mapped information onto subunits to discern affected processes. Across patient cohort (consisting organic acidaemias, fatty acid...
Recently, the GlyConnect-oxime (GC) protein conjugation strategy was developed to provide a site-selective glycan-based as an extension in-house GlycoDelete (GD) technology. GD gives access glycoproteins with single GlcNAc, LacNAc, or LacNAc-Sia type glycans on their N-glycosylation sites. We have previously shown that these unique handle for they short, homogeneous and hydrophilic link backbone. GC focused use of chemical chemo-enzymatic pathways molecule interest via oxime formation...