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Patients with chronic hepatitis C virus (HCV) infection have a genuine risk of developing liver fibrosis and cirrhosis, potentially resulting in hepatocellular carcinoma (HCC), a risk that remains even after sustained viral response (SVR). Glycomics-based biomarkers are an attractive tool to closely monitor these patients during and after antiviral treatment, as alterations in the abundance of N-glycans reflect an altered state of the liver. This study assessed serum glycomics for the evaluation of inflammation-related fibrosis regression during and after treatment of HCV with DAAs.The GlycoFibroTest and GlycoCirrhoTest were analyzed in the sera 36 HCV-infected patients with advanced fibrosis (F3) or established cirrhosis (F4), before (week 0), during (week 12) and after (week 24) a twelve-week oral administration of DAAs therapy - using an optimized glycomic technology on a DNA sequencer.All patients achieved SVR after treatment and two of them developed HCC in the subsequent five years. A significant decrease of the GlycoFibroTest (p 0.0001) was seen after 12 weeks, consistent with other measured biomarkers (APRI, FIB-4, FibroTest). Statistical analysis was performed in IBM SPSS Statistics version 28.0, using the non-parametric Friedman's test with a statistical significance α level of 0.05.This study suggests that the GlycoFibroTest is a serum biomarker for viral response in HCV patients. The rapid decrease of the glycomics-based biomarker probably reflects the amelioration of liver inflammation as underlying process, rather than the improvement of liver fibrosis itself.

This file gives additional information regarding the GlycoCirrhoTest and other glycomics-based test based on the same technology (DSA-FACE) for glycomic analysis.

The ongoing COVID-19 pandemic has emphasized the urgent need for rapid, accurate, and large-scale diagnostic tools. Next to this, the significance of serological tests (i.e., detection of SARS-CoV-2 antibodies) also became apparent for studying patients' immune status and past viral infection. In this work, we present a novel approach for not only measuring antibody levels but also profiling of binding kinetics of the complete polyclonal antibody response against the receptor binding domain (RBD) of SARS-CoV-2 spike protein, an aspect not possible to achieve with traditional serological tests. This fiber optic surface plasmon resonance (FO-SPR)-based label-free method was successfully accomplished in COVID-19 patient serum and, for the first time, directly in undiluted whole blood, omitting the need for any sample preparation. Notably, this bioassay (1) was on par with FO-SPR sandwich bioassays (traditionally regarded as more sensitive) in distinguishing COVID-19 from control samples, irrespective of the type of sample matrix, and (2) had a significantly shorter time-to-result of only 30 min compared to >1 or 4 h for the FO-SPR sandwich bioassay and the conventional ELISA, respectively. Finally, the label-free approach revealed that no direct correlation was present between antibody levels and their kinetic profiling in different COVID-19 patients, as another evidence to support previous hypothesis that antibody-binding kinetics against the antigen in patient blood might play a role in the COVID-19 severity. Taking all this into account, the presented work positions the FO-SPR technology at the forefront of other COVID-19 serological tests, with a huge potential toward other applications in need for quantification and kinetic profiling of antibodies. ispartof: ACS SENSORS vol:7 issue:2 pages:477-487 ispartof: location:United States status: published

Recently, the GlyConnect-oxime (GC) protein conjugation strategy was developed to provide a site-selective glycan-based conjugation strategy as an extension to the in-house developed GlycoDelete (GD) technology. GD gives access to glycoproteins with single GlcNAc, LacNAc, or LacNAc-Sia type glycans on their

Recently, chimeric antigen receptor (CAR) T cell technology has revolutionized cancer immunotherapy. This strategy uses synthetic CARs to redirect T cells to specific antigens expressed on the surface of tumor cells. Despite impressive progress in the treatment of hematological malignancies with CAR T cells, scientific challenges still remain for use of CAR T cell therapy to treat solid tumors. This is mainly due to the hostile tumor microenvironment and CAR-related toxicities. As the glycans decorating the T cell surface are implicated in T cell activation, differentiation, proliferation, and in the interaction of human T cells with tumor cells, we studied the role of human T cell glycosylation in more depth by manipulating their glycome. In this context, there isin vitroevidence that β-galactoside binding lectins (Galectins) can have a strong impact on the functionality of tumor-infiltrating T cells. The high-affinity poly-LacNAc N-linked galectin ligands are mainly synthesized onto the β1,6-GlcNAc branch introduced by N-acetylglucosaminyltransferase V (GnTV, encoded byMgat5). We showed that knocking outMgat5in CD70 targeting CAR T cells leads to lower densities of poly-LacNAc modifications on the CAR T cell surface. Most interestingly, our results indicate that MGAT5 KO CD70 CAR T cells show enhanced potency to control primary tumors and relapses.

In the standard toolkit for recombinant protein expression, the yeast known in biotechnology asPichia pastoris(formally:Komagataella phaffii) takes up the position betweenE. coliand HEK293 or CHO mammalian cells, and is used by thousands of laboratories both in academia and industry. The organism is eukaryotic yet microbial, and grows to extremely high cell densities while secreting proteins into its fully defined growth medium, using very well established strong inducible or constitutive promoters. Many products made inPichiaare in the clinic and in industrial markets.Pichiais also a favoured host for the rapidly emerging area of ‘precision fermentation’ for the manufacturing of food proteins. However, the earliest steps in the development of the industrial strain (NRRL Y-11430/CBS 7435) that is used throughout the world were performed prior to 1985 in industry (Phillips Petroleum Company) and are not in the public domain. Moreover, despite the long expiry of associated patents, the patent deposit NRRL Y-11430/CBS 7435 that is the parent to all commonly used industrial strains, is not or no longer made freely available through the resp. culture collections. This situation is far from ideal for what is a major chassis for synthetic biology, as it generates concern that novel applications of the system are still encumbered by licensing requirements of the very basic strains. In the spirit of open science and freedom to operate for what is a key component of biotechnology, we set out to resolve this by using genome sequencing of type strains, reverse engineering where necessary, and comparative protein expression and strain characterisation studies. We find that the industrial strains derive from theK. phaffiitype strain lineage deposited as 54-11.239 in the UC Davis Phaff Yeast Strain collection by Herman Phaff in 1954. This type strain has valid equivalent deposits that are replicated/derived from it in other yeast strain collections, incl. in ARS-NRRL NRRL YB-4290 (deposit also made by Herman Phaff) and NRRL Y-7556, CBS 2612 and NCYC 2543. We furthermore discovered that NRRL Y-11430 and its derivatives carry an ORF-truncating mutation in theHOC1cell wall synthesis gene, and that reverse engineering of a similar mutation in the NCYC 2543 type strain imparts the high transformability that is characteristic of the industrial strains. Uniquely, the NCYC 2543 type strain, which we propose to call ‘OPENPichia’ henceforth, is freely available from the NCYC culture collection, incl. resale and commercial production licenses at nominal annual licensing fees1. Furthermore, our not-for-profit research institute VIB has also acquired a resale/distribution license from NCYC, which we presently use to openly provide to end-users our genome-sequenced OPENPichia subclone strain and its derivatives, i.e., currently the highly transformablehoc1trand thehis4auxotrophic mutants. To complement the OPENPichia platform, a fully synthetic modular gene expression vector building toolkit was developed, which is also openly distributed, for any purpose. We invite other researchers to contribute to our open science resource-building effort to establish a new unencumbered standard chassis forPichiasynthetic biology.

MotivationWith a regulatory impact on numerous biological processes, protein phosphorylation is one of the most studied post-translational modifications. Effective computational methods that provide a sequence-based prediction of phosphorylation sites are desirable to guide functional experiments. Currently, the most successful methods train neural networks on amino acid composition representations. However, recently proposed protein language models provide enriched sequence representations that contain higher-level pattern information on which more performant phosphorylation site predictions may be based.ResultsWe explored the applicability of protein language models to general phosphorylation site prediction. We found that training prediction models on top of protein language models yield a relative improvement of up to 68.4% in terms of area under the precision-recall curve over the state-of-the-art predictors. Model interpretation and model transferability experiments reveal that protease-specific cleavage patterns give rise to a protease-specific training bias. This can result in an overly optimistic estimation of phosphorylation site prediction performance, an important caveat in the application of advanced machine learning approaches to protein modification prediction based on proteomics data. We show that improving data quality by negative sample filtering using experimental metadata can mitigate this problem.Availability and implementationThe PhosphoLingo tool, with trained models, code, models, datasets, and predictions are available athttps://github.com/jasperzuallaert/PhosphoLingo.Contactsven.degroeve@vib-ugent.beSupplementary informationSupplementary materials are available atbioRxiv.

Background: Chloride measurement is crucial for calculating the anion gap. Bicarbonate can interfere with chloride measurements; however, there is no information on the specific types of electrodes affected or the changes in bicarbonate non-selectivity over time. We evaluated the interference of bicarbonate on chloride measurements using different electrodes and the stability of this interference over time. Methods: The effect of bicarbonate on chloride measured with electrodes of various manufacturers was assessed. When non-selectivity toward bicarbonate was observed, the stability of this interference during the electrode's lifetime was explored. The impact of the bicarbonate concentration on the calibrator was also evaluated. Results: Non-selectivity was observed for electrodes using quaternary ammonium salts (Beckman Coulter, Siemens, and Roche), with overestimated or underestimated chloride values observed at high or low bicarbonate concentrations, respectively. The degree of selectivity varied among electrodes. With the Roche electrode, interference became more pronounced over time, whereas the Siemens electrode appeared to gain selectivity during its lifetime. For the Roche system, adjusting the calibrator's bicarbonate concentration from 30 mmol/L to 20-24 mmol/L reduced the number of samples with unacceptable bias ( >3%) from 77.3% to 12.6%. Lot-to-lot variations in the calibrator bicarbonate concentration increased the uncertainty of chloride measurements. Conclusions: The extent of bicarbonate-induced error varied according to the type, manufacturer, and wear of the electrode; the bicarbonate concentration in the calibrators and the tested sample; and the chloride content. Laboratories should be aware of the impact of bicarbonate on routine chloride measurements to establish appropriate QC procedures.

Only few biomarkers have been evaluated for their prognostic value following radical prostatectomy. We explored if tissue N-glycosylation shows prognostic properties for biochemical recurrence (BCR...

The structural organization of the Golgi stacks in mammalian cells is intrinsically linked to function, including glycosylation, but the role of morphology is less clear in lower eukaryotes. Here we investigated the link between the structural organization of the Golgi and secretory pathway function using Pichia pastoris as a model system. To unstack the Golgi cisternae, we disrupted 18 genes encoding proteins in the secretory pathway without loss of viability. Using biosensors, confocal microscopy and transmission electron microscopy we identified three strains with irreversible perturbations in the stacking of the Golgi cisternae, all of which had disruption in genes that encode proteins with annotated function as or homology to calcium/calcium permeable ion channels. Despite this, no variation in the secretory pathway for ER size, whole cell glycomics or recombinant protein glycans was observed. Our investigations showed the robust nature of the secretory pathway in P. pastoris and suggest that Ca2+ concentration, homeostasis or signalling may play a significant role for Golgi stacking in this organism and should be investigated in other organisms.

As small and stable high-affinity antigen binders, VHHs boast attractive characteristics both for therapeutic use in various disease indications, and as versatile reagents in research and diagnostics. To further increase the versatility of VHHs, we explored the VHH scaffold in a structure-guided approach to select regions where the introduction of an N-glycosylation N-X-T sequon and its associated glycan should not interfere with protein folding or epitope recognition. We expressed variants of such glycoengineered VHHs in the Pichia pastoris GlycoSwitchM5 strain, allowing us to pinpoint preferred sites at which Man5GlcNAc2-glycans can be introduced at high site occupancy without affecting antigen binding. A VHH carrying predominantly a Man5GlcNAc2 N-glycan at one of these preferred sites showed highly efficient, glycan-dependent uptake by Mf4/4 macrophages in vitro and by alveolar lung macrophages in vivo, illustrating one potential application of glyco-engineered VHHs: a glycan-based targeting approach for lung macrophage endolysosomal system delivery. The set of optimal artificial VHH N-glycosylation sites identified in this study can serve as a blueprint for targeted glyco-engineering of other VHHs, enabling site-specific functionalization through the rapidly expanding toolbox of synthetic glycobiology.

The aim of this exploratory clinical study was to evaluate whether the preanalytical quality of blood samples subjected to delayed centrifugation and transport - as a result of home-sampling - is affected in a way it alters the clinical decision-making for patients under systemic cancer therapy. This evaluation is part of a comprehensive investigation of the opportunities for oncological home-hospitalization. Forty-nine patients with cancer donated two additional blood samples during their ambulatory hospital visit. Fifteen blood analytes were compared between routine blood samples and samples that were subjected to transport and delayed centrifugation in order to mimic a locally implemented model for oncological home-hospitalisation. Deviations were analysed by means of Deming regression. For those analytes showing statistically significant intercepts and/or slopes, the mean deviations were compared to the desirable analytical bias; and the intra-individual differences were compared with the limits for clinical decision-making. Statistically significant intercepts and/or slopes were observed for haematocrit (HCT), mean cellular volume (MCV), platelets count (PLT) and C-reactive protein (CRP). Differences exceeding the allowable margins of desirable analytical bias were observed for HCT and MCV. Risk of different clinical decision-making couldn't be observed for any of the analytes showing statistically significant differences. These results demonstrate that home-collection of blood samples, transported at room temperature and centrifuged within a mean time of five hours after sampling, has no effect on clinical decision-making with regards to systemic cancer therapy. However, attention should be paid to the potential occurrence of haemolysis during the preanalytical phase, which can negatively influence haemolysis-dependent variables.

The deoxy sugar l-fucose is frequently found as a glycan constituent on and outside living cells, and in mammals it is involved in a wide range of biological processes including leukocyte trafficking, histo-blood group antigenicity and antibody effector functions. The manipulation of fucose levels in those biomedically important systems may provide novel insights and therapeutic leads. However, despite the large established sequence diversity of natural fucosidases, so far, very few enzymes have been characterized. We explored the diversity of the α-l-fucosidase-containing CAZY family GH29 by bio-informatic analysis, and by the recombinant production and exploration for fucosidase activity of a subset of 82 protein sequences that represent the family’s large sequence diversity. After establishing that most of the corresponding proteins can be readily expressed in E. coli, more than half of the obtained recombinant proteins (57% of the entire subset) showed activity towards the simple chromogenic fucosylated substrate 4-nitrophenyl α-l-fucopyranoside. Thirty-seven of these active GH29 enzymes (and the GH29 subtaxa that they represent) had not been characterized before. With such a sequence diversity-based collection available, it can easily be used to screen for fucosidase activity towards biomedically relevant fucosylated glycoproteins. As an example, the subset was used to screen GH29 members for activity towards the naturally occurring sialyl-Lewis x-type epitope on glycoproteins, and several such enzymes were identified. Together, the results provide a significant increase in the diversity of characterized GH29 enzymes, and the recombinant enzymes constitute a resource for the further functional exploration of this enzyme family.

In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in paediatric oncology in a cost-effective and minimally invasive manner.

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing COVID-19 pandemic. To prevent the massive COVID-19 burden, several vaccination campaigns were initiated. We performed a single center observational trial to evaluate adaptive immunity in naive healthcare workers upon BNT162b2 vaccination.MethodsSerological analysis was performed through conventional immunoassays. Antibody functionality was analyzed via in vitro neutralization assays. Circulating receptor-binding domain (RBD) specific B cells were assessed via flowcytometry. The induction of SARS-CoV-2 specific T cells was investigated through interferon-γ release assay combined with flowcytometric profiling of activated CD4 and CD8 T cells.ResultsThree months after vaccination, all but one of the subjects (N = 31) displayed vaccine-induced neutralizing antibodies. In 10 out of 31 subjects, circulating RBD specific B cells were found of which the rate showed moderate correlation to serological parameters. Specific interferon-γ release was present in all subjects and correlated with the significant upregulation of CD69 on CD4+ and CD8+ T cells and CD40L on CD4+ T cells. Interestingly, no relation was found between B and T cell parameters. In addition, one symptomatic breakthrough infection with the SARS-CoV-2 alpha variant of concern was reported.ConclusionThree months post vaccination, both humoral and cellular immune responses are detectable in all but one participant. No correlation was found between the magnitude of both B and T cell responses.

For a long time, glycoprotein production has been limited by the inherent properties of production hosts. Glycosylation of biopharmaceuticals has been regarded as a necessary evil, often needed for protein folding or function, but also a source of heterogeneity, complicating downstream processing and product characterization. This has strongly determined the choice of production hosts. Over the last few decades, numerous glycoengineering efforts have helped solving this problem. Moreover, insights from fundamental studies have made it possible to improve therapeutic protein functionality through careful glycoengineering. Here, we will focus on how production host and in vitro glycoengineering approaches allow to design biopharmaceuticals with glycans that impart improved functionality. An important branch of research explores how glycosylation can be tuned to improve pharmacokinetics and reduce glycan heterogeneity of therapeutics. Furthermore, antibody glycoengineering to obtain homogeneous, defined glycan structures has been a major focus. An example of this is the production of Fc glycans without core fucose, exhibiting tremendously improved Antibody-Dependent Cell Cytotoxicity (ADCC). In the last part, glycoforms that allow for improved (subcellular) targeting and cellular uptake, a field that opens possibilities for enzyme replacement therapies and vaccine development, will be highlighted.

SARS-CoV-2 B.1.1.529, designated omicron, was recently identified as a new variant of concern by WHO and is rapidly replacing SARS-CoV-2 delta as the most dominant variant in many countries. Unfortunately, because of the high number of mutations present in the spike of SARS-CoV-2 omicron, most monoclonal antibodies (mAbs) currently approved for treatment of COVID-19 lose their in vitro neutralizing activity against this variant. We recently described a panel of human anti-SARS-CoV-2 mAbs that potently neutralize SARS-CoV-2 Wuhan, D614G and variants alpha, beta, gamma and delta. In this work, we evaluated our mAb panel for potential in vitro activity against SARS-CoV-2 delta and omicron. Three mAbs from our panel retain neutralizing activity against both delta and omicron, with mAb 3B8 still resulting in complete neutralization at a concentration as low as 0.02 μg/ml for both variants. Overall, our data indicate that mAb 3B8 may have the potential to become a game-changer in the fight against the continuously evolving SARS-CoV-2.

Treatment with neutralizing monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contributes to COVID-19 management. Unfortunately, SARS-CoV-2 variants escape several of these recently approved mAbs, highlighting the need for additional discovery and development. In a convalescent patient with COVID-19, we identified six mAbs, classified in four epitope groups, that potently neutralized SARS-CoV-2 D614G, beta, gamma, and delta infection in vitro, with three mAbs neutralizing omicron as well. In hamsters, mAbs 3E6 and 3B8 potently cured infection with SARS-CoV-2 Wuhan, beta, and delta when administered post-viral infection at 5 mg/kg. Even at 0.2 mg/kg, 3B8 still reduced viral titers. Intramuscular delivery of DNA-encoded 3B8 resulted in in vivo mAb production of median serum levels up to 90 μg/mL, and protected hamsters against delta infection. Overall, our data mark 3B8 as a promising candidate against COVID-19, and highlight advances in both the identification and gene-based delivery of potent human mAbs. ispartof: ISCIENCE vol:25 issue:8 ispartof: location:United States status: published

Treatment with neutralizing monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contributes to COVID-19 management. Unfortunately, SARS-CoV-2 variants can escape several of these recently approved mAbs, highlighting the need for additional discovery and development. In a convalescent COVID-19 patient, we identified six mAbs, classified in four epitope groups, that potently neutralized SARS-CoV-2 Wuhan, alpha, beta, gamma and delta infection in vitro. In hamsters, mAbs 3E6 and 3B8 potently cured infection with SARS-CoV-2 Wuhan, beta and delta when administered post-viral infection at 5 mg/kg. Even at 0.2 mg/kg, 3B8 still reduced viral titers. Intramuscular delivery of DNA-encoded 3B8 resulted in in vivo mAb production of median serum levels up to 90 μg/ml, and protected hamsters against delta infection. Overall, our data mark 3B8 as a promising candidate against COVID-19, and highlight advances in both the identification and gene-based delivery of potent human mAbs.

Broadly neutralizing antibodies are an important treatment for individuals with coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Antibody-based therapeutics are also essential for pandemic preparedness against future Sarbecovirus outbreaks. Camelid-derived single domain antibodies (VHHs) exhibit potent antimicrobial activity and are being developed as SARS-CoV-2–neutralizing antibody-like therapeutics. Here, we identified VHHs that neutralize both SARS-CoV-1 and SARS-CoV-2, including now circulating variants. We observed that the VHHs bound to a highly conserved epitope in the receptor binding domain of the viral spike protein that is difficult to access for human antibodies. Structure-guided molecular modeling, combined with rapid yeast-based prototyping, resulted in an affinity enhanced VHH-human immunoglobulin G1 Fc fusion molecule with subnanomolar neutralizing activity. This VHH-Fc fusion protein, produced in and purified from cultured Chinese hamster ovary cells, controlled SARS-CoV-2 replication in prophylactic and therapeutic settings in mice expressing human angiotensin converting enzyme 2 and in hamsters infected with SARS-CoV-2. These data led to affinity-enhanced selection of the VHH, XVR011, a stable anti–COVID-19 biologic that is now being evaluated in the clinic. ispartof: SCIENCE TRANSLATIONAL MEDICINE vol:13 issue:621 ispartof: location:United States status: published

Background: Acute kidney injury (AKI) in critically ill patients is associated with a significant increase in mortality as well as long-term renal dysfunction and chronic kidney disease (CKD). Serum creatinine (SCr), the most widely used biomarker to evaluate kidney function, does not always accurately predict the glomerular filtration rate (GFR), since it is affected by some non-GFR determinants such as muscle mass and recent meat ingestion. Researchers and clinicians have gained interest in cystatin C (CysC), another biomarker of kidney function. The study objective was to compare GFR estimation using SCr and CysC in detecting CKD over a 1-year follow-up after an AKI stage-3 event in the ICU, as well as to analyze the association between eGFR (using SCr and CysC) and mortality after the AKI event. Method: This prospective observational study used the medical records of ICU patients diagnosed with AKI stage 3. SCr and CysC were measured twice during the ICU stay and four times following diagnosis of AKI. The eGFR was calculated using the EKFC equation for SCr and FAS equation for CysC in order to check the prevalence of CKD (defined as eGFR < 60 mL/min/1.73 m2). Results: The study enrolled 101 patients, 36.6% of whom were female, with a median age of 74 years (30−92), and a median length of stay of 14.5 days in intensive care. A significant difference was observed in the estimation of GFR when comparing formulas based on SCrand CysC, resulting in large differences in the prediction of CKD. Three months after the AKI event, eGFRCysC < 25 mL/min/1.73 m2 was a predictive factor of mortality later on; however, this was not the case for eGFRSCr. Conclusion: The incidence of CKD was highly discrepant with eGFRCysC versus eGFRSCr during the follow-up period. CysC detects more CKD events compared to SCr in the follow-up phase and eGFRCysC is a predictor for mortality in follow-up but not eGFRSCr. Determining the proper marker to estimate GFR in the post-ICU period in AKI stage-3 populations needs further study to improve risk stratification. ispartof: Journal Of Clinical Medicine vol:11 issue:24 ispartof: location:Switzerland status: Published online

The chytrid fungal pathogens Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans cause the skin disease chytridiomycosis in amphibians, which is driving a substantial proportion of an entire vertebrate class to extinction. Mitigation of its impact is largely unsuccessful and requires a thorough understanding of the mechanisms underpinning the disease ecology. By identifying skin factors that mediate key events during the early interaction with B. salamandrivorans zoospores, we discovered a marker for host colonization. Amphibian skin associated beta-galactose mediated fungal chemotaxis and adhesion to the skin and initiated a virulent fungal response. Fungal colonization correlated with the skin glycosylation pattern, with cutaneous galactose content effectively predicting variation in host susceptibility to fungal colonization between amphibian species. Ontogenetic galactose patterns correlated with low level and asymptomatic infections in salamander larvae that were carried over through metamorphosis, resulting in juvenile mortality. Pronounced variation of galactose content within some, but not all species, may promote the selection for more colonization resistant host lineages, opening new avenues for disease mitigation., The skin disease chytridiomycosis is linked to global amphibian declines but effective mitigation measures require improved understanding of the mechanisms underpinning the disease ecology. This study identifies key mediators of interactions between the fungal pathogen and amphibian skin, providing a marker of host colonization that can predict susceptibility between amphibian species.

Recently, our lab developed GlycoDelete, a technology suite that allows a radical simplification of eukaryotic N-glycosylation. The technology allows to produce glycoproteins that carry single GlcNAc, LacNAc, or LacNAc-Sia type glycans on their N-linked glycosylation sequons. GlycoDelete-type N-glycans are uniquely suited for glycan-based conjugation purposes, as these provide a short, homogeneous and hydrophilic link to the protein backbone. Targeting GlycoDelete-glycans allows for highly site-specific conjugation at sites in the protein which are normally occupied by bulky glycans, thus ensuring minimal interference with protein structure and function. The current manuscript describes the evaluation and optimization of both chemical and chemo-enzymatic conjugation of molecules onto the GlycoDelete-type glycans of a limited set of benchmark proteins.

The genus Mycobacterium includes several pathogens that cause severe disease in humans, like Mycobacterium tuberculosis (M. tb), the infectious agent causing tuberculosis. Genetic tools to engineer mycobacterial genomes, in a targeted or random fashion, have provided opportunities to investigate M. tb infection and pathogenesis. Furthermore, they have allowed the identification and validation of potential targets for the diagnosis, prevention, and treatment of tuberculosis. This review describes the various methods that are available for the generation of mutants in Mycobacterium species, focusing specifically on tools for altering slow-growing mycobacteria from the M. tb complex. Among others, it incorporates the recent new molecular biological technologies (e.g. ORBIT) to rapidly and/or genome-wide comprehensively obtain targeted mutants in mycobacteria. As such, this review can be used as a guide to select the appropriate genetic tools to generate mycobacterial mutants of interest, which can be used as tools to aid understanding of M. tb infection or to help developing TB intervention strategies.

Background Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172–1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172–1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. Results By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. Conclusions We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization. Electronic supplementary material The online version of this article (10.1186/s12864-019-5909-5) contains supplementary material, which is available to authorized users.