Diagnosing COVID-19; towards a feasible COVID-19 rule-out protocol.

INTRODUCTION: We present the results of the COVID-19 rule-out protocol at Ghent University Hospital, a step-wise testing approach which included repeat NFS SARS-CoV-2 rRT-PCR, respiratory multiplex RT-PCR, low-dose chest CT and bronchoscopy with BAL to confirm or rule-out SARS-CoV-2 infection in patients admitted with symptoms suggestive of COVID-19. RESULTS: Between 19 March 2020 and 30 April 2020, 455 non-critically ill patients with symptoms suspect for COVID-19 were admitted. The initial NFS for SARS-CoV-2 rRT-PCR yielded 66.9%, the second NFS 25.4% and bronchoscopy with BAL 5.9% of total COVID-19 diagnoses. In the BAL fluid, other respiratory pathogens were detected in 65% (13/20) of the COVID-19 negative patients and only in 1/7 COVID-19 positive patients. Retrospective antibody testing at the time around BAL sampling showed a positive IgA or IgG in 42.9 % of the COVID-19 positive and 10.5% of the COVID-19 negative group. Follow-up serology showed 100% COVID-19 positivity in the COVID-19 positive group and 100% IgG negativity in the COVID-19 negative group. CONCLUSION: In our experience, bronchoscopy with BAL can have an added value to rule-in or rule-out COVID-19 in patients with clinical and radiographical high-likelihood of COVID-19 and repeated negative NFS testing. Furthermore, culture and respiratory multiplex PCR on BAL fluid can aid to identify alternative microbial etiological agents in this group. Retrospective analysis of antibody development in this selected group of patients suggests that the implementation of serological assays in the routine testing protocol will decrease the need for invasive procedures like bronchoscopy.

In vitro stability and ex vivo absorption of thymol monoglucosides in the porcine gut.

Thymol α-D-glucopyranoside (TαG) and thymol ß-D-glucopyranoside (TßG) are believed to have different kinetic behaviours in the porcine gut than its parent aglycon thymol. However, recently, it was shown that concentrations of both glucosides decreased rapidly in the stomach and proximal small intestine following oral supplementation to piglets as did thymol. Yet, the stability of thymol glucosides in gut contents and their absorption route remains obscure. Therefore, a series of in vitro incubations were performed, simulating the impact of pH, digestive enzymes, bacterial activity and mucosal extracts on stability of these glucosides. Their absorption mechanisms were investigated using the Ussing chamber model in the presence or the absence of inhibitors of sodium-dependent glucose linked transporter 1 and lactase phlorizin hydrolase. Both glucosides remained intact at physiological pH levels in the presence of digestive enzymes. Recoveries from TαG and TßG were below 90% when incubated with small intestinal homogenates from the distal jejunum or from all sampled sites, respectively. However, no aglycon could be detected in these samples. Bacterial inoculum of the small intestine, on the other hand, hydrolysed TßG quickly with up to 44% of free aglycon appearing. TαG proved more resistant to porcine gastro-intestinal bacterial glucosidases with only trace amounts (<1%) of free thymol at the end of the incubations. Electrophysiological measurements in Ussing chambers did not suggest active transport of the glucosides. Mucosal TαG and TßG concentrations were unchanged between start and end of the absorption measurements. Additionally, no TαG and only a very limited amount of TßG were retrieved from the serosal side. Tissue associated concentrations, although marginal (<1% of luminal concentration), were mainly as intact glucoside or as aglycon for TαG and TßG, respectively. Addition of both inhibitors significantly increased the amount of intact glucosides retrieved from the mucosal tissues as compared to controls. In conclusion, bacterial hydrolysis was identified as the most important source of TßG loss, whereas TαG seemed less prone to degradation or absorption in these in vitro and ex vivo models.

Double protein-coated poly-ε-caprolactone scaffolds: successful 2D to 3D transfer.

In the past decade, tissue engineering has evolved from a promising technology to an established scientific field. Large attention has focussed on developing scaffolds from both biodegradable and nondegradable polymers to be cultivated with cells, to replace human body defects. The major drawback of most polymers is however their limited cell-interactive properties. An additional complication when developing a surface modification protocol for those materials is the transferability of protocols from 2D substrates to 3D scaffolds. In the present work, we therefore report on possible biological effects originating from the transfer of a double protein coating protocol, involving gelatin type B and fibronectin, from 2D poly-ε-caprolactone (PCL) films to 3D PCL scaffolds produced by rapid prototyping. A variety of techniques including scanning electron microscopy, X-ray photoelectron spectroscopy and confocal fluorescence microscopy confirmed a successful and homogeneous protein-coating on both 2D and 3D substrates. Interestingly, the biological performance of the double protein-coated PCL substrates, reflected by the initial cell adhesion, proliferation, and colonization was superior compared to the other surface modification steps, independent of the material dimension.

Label-free magnetic resonance imaging to locate live cells in three-dimensional porous scaffolds.

Porous scaffolds are widely tested materials used for various purposes in tissue engineering. A critical feature of a porous scaffold is its ability to allow cell migration and growth on its inner surface. Up to now, there has not been a method to locate live cells deep inside a material, or in an entire structure, using real-time imaging and a non-destructive technique. Herein, we seek to demonstrate the feasibility of the magnetic resonance imaging (MRI) technique as a method to detect and locate in vitro non-labelled live cells in an entire porous material. Our results show that the use of optimized MRI parameters (4.7 T; repetition time = 3000 ms; echo time = 20 ms; resolution 39 × 39 µm) makes it possible to obtain images of the scaffold structure and to locate live non-labelled cells in the entire material, with a signal intensity higher than that obtained in the culture medium. In the current study, cells are visualized and located in different kinds of porous scaffolds. Moreover, further development of this MRI method might be useful in several three-dimensional biomaterial tests such as cell distribution studies, routine qualitative testing methods and in situ monitoring of cells inside scaffolds.

Double protein functionalized poly-ε-caprolactone surfaces: in depth ToF-SIMS and XPS characterization.

In biomaterial research, great attention has focussed on the immobilization of biomolecules with the aim to increase cell-adhesive properties of materials. Many different strategies can be applied. In previously published work, our group focussed on the treatment of poly-ε-caprolactone (PCL) films by an Ar-plasma, followed by the grafting of 2-aminoethyl methacrylate (AEMA) under UV-irradiation. The functional groups introduced, enabled the subsequent covalent immobilisation of gelatin. The obtained coating was finally applied for the physisorption of fibronectin. The successful PCL surface functionalization was preliminary confirmed using XPS, wettability studies, AFM and SEM. In the present article, we report on an in-depth characterization of the materials developed using ToF-SIMS and XPS analysis. The homogeneous AEMA grafting and the subsequent protein coating steps could be confirmed by both XPS and ToF-SIMS. Using ToF-SIMS, it was possible to demonstrate the presence of polymethacrylates on the surface. From peak deconvoluted XPS results (C- and N-peak), the presence of proteins could be confirmed. Using ToF-SIMS, different positive ions, correlating to specific amino-acids could be identified. Importantly, the gelatin and the fibronectin coatings could be qualitatively distinguished. Interestingly for biomedical applications, ethylene oxide sterilization did not affect the surface chemical composition. This research clearly demonstrates the complementarities of XPS and ToF-SIMS in biomedical surface modification research.

Development and application of a screening assay for glycoside phosphorylases.

Glycoside phosphorylases (GPs) are interesting enzymes for the glycosylation of chemical molecules. They require only a glycosyl phosphate as sugar donor and an acceptor molecule with a free hydroxyl group. Their narrow substrate specificity, however, limits the application of GPs for general glycoside synthesis. Although an enzyme's substrate specificity can be altered and broadened by protein engineering and directed evolution, this requires a suitable screening assay. Such a screening assay has not yet been described for GPs. Here we report a screening procedure for GPs based on the measurement of released inorganic phosphate in the direction of glycoside synthesis. It appeared necessary to inhibit endogenous phosphatase activity in crude Escherichia coli cell extracts with molybdate, and inorganic phosphate was measured with a modified phosphomolybdate method. The screening system is general and can be used to screen GP enzyme libraries for novel donor and acceptor specificities. It was successfully applied to screen a residue E649 saturation mutagenesis library of Cellulomonas uda cellobiose phosphorylase (CP) for novel acceptor specificity. An E649C enzyme variant was found with novel acceptor specificity toward alkyl beta-glucosides and phenyl beta-glucoside. This is the first report of a CP enzyme variant with modified acceptor specificity.

An elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy.

An in silico survey of all known 3D-structures of glycoside hydrolases that contain a ligand in the -1 subsite is presented. A recurrent crucial positioning of active site residues indicates a common general strategy for electrostatic stabilisation directed to the carbohydrate's ring-oxygen at the transition state. This is substantially different depending on whether the enzyme's proton donor is syn or anti positioned versus the substrate. A comprehensive list of enzymes belonging to 42 different families is given and selected examples are described. An implication for an early evolution scenario of glycoside hydrolases is discussed.

A hydrophobic platform as a mechanistically relevant transition state stabilising factor appears to be present in the active centre of all glycoside hydrolases.

An in silico survey of the -1 subsite of all known 3D-structures of O-glycoside hydrolases containing a suitably positioned ligand has led to the recognition -- apparently without exceptions -- of a transition state stabilising hydrophobic platform which is complementary to a crucial hydrophobic patch of the ligand. This platform is family-specific and highly conserved. A comprehensive list is given with examples of enzymes belonging to 33 different families. Several typical constellations of platform - protein residues are described.

Novel tools for the study of class I alpha-mannosidases: a chromogenic substrate and a substrate-analog inhibitor.

The use of chromogenic substrates for evaluation of class I alpha-mannosidase is described. 2('),4(')-Dinitrophenyl-alpha-D-mannopyranoside allows rapid and sensitive assays of enzymatic activities, e.g., of heterologously expressed alpha-1,2-mannosidase from Trichoderma reesei. Interaction constants of several ligands with alpha-mannosidases from class I and II could also be determined. Furthermore, novel types of inhibitors derived from D-lyxose are presented. Methyl-alpha-D-lyxopyranosyl-(1(')-->2)-alpha-D-mannopyranoside is a potent inhibitor of the alpha-1,2-mannosidase from T. reesei (K(i)=600 microM) and since it probably spans subsites -1/+1, this disaccharide could be valuable in crystallographic studies of class I alpha-mannosidases.

The development of working memory: exploring the complementarity of two models.

The aim of the paper was to further explore the complementarity of the working memory models postulated by Pascual-Leone and Baddeley. Five-, six-, eight-, and nine-year-old children were assessed on two working memory tasks that have frequently been used within the respective streams of research: the Mr. Peanut task and the Corsi blocks task. Results indicated a developmental increase in spatial short-term memory for both tasks. Concurrent spatial suppression reduced performance on the two tasks in all four age groups. By contrast, articulatory suppression interfered with recall only on the Mr. Peanut task, and in only the older children. The two models were shown to make their own specific contribution to the interpretation of the data, attesting to their complementarity. Pascual-Leone's theory offered a clear explanation of the results concerning the central aspects of working memory, that is, the stepwise age-related increase in performance, whereas Baddeley's model provided a convincing account of the findings regarding the peripheral phonological and visuo-spatial components, that is, the effects of articulatory and spatial suppression.