Standard SARS-CoV-2 testing protocols using nasopharyngeal/throat (NP/T) swabs are invasive and require trained medical staff for reliable sampling. In addition, it has been shown that PCR is more sensitive as compared to antigen-based tests. Here we describe the analytical and clinical evaluation of our in-house RNA extraction-free saliva-based molecular assay for the detection of SARS-CoV-2. Analytical sensitivity of the test was equal to the sensitivity obtained in other Dutch diagnostic laboratories that process NP/T swabs. In this study, 955 individuals participated and provided NP/T swabs for routine molecular analysis (with RNA extraction) and saliva for comparison. Our RT-qPCR resulted in a sensitivity of 82,86% and a specificity of 98,94% compared to the gold standard. A false-negative ratio of 1,9% was found. The SARS-CoV-2 detection workflow described here enables easy, economical, and reliable saliva processing, useful for repeated testing of individuals.
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Het Genomisch kookboek is een boekje waarin moleculair biologische processen worden geïllustreerd met behulp van metaforen rondom koken.
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The NANOSPRESSO project is a pioneering response to the complex challenge of treating orphan diseases, which, despite affecting millions of people globally, have only scant therapeutic options. This initiative represents a paradigm shift by decentralizing the production of personalized nucleic acid nanomedicines. Integrating advanced microfluidic technology with lipid nanoparticle engineering platforms—validated by their efficacy in COVID-19 messenger (m)RNA vaccines— the NANOSPRESSO model enables hospital pharmacists to seamlessly assemble tailored therapeutic cartridges for gene/RNA therapy administration at the patient’s bedside. This innovative model subverts the traditional constraints of high-cost, intricate manufacturing and the instability of nucleic acid-based treatments, offering a streamlined. localized, flexible, and patient-centric alternative. Inspired by the traditional art of compounding in pharmacy, NANOSPRESSO strives to democratize access to innovative treatments for rare diseases, challenging the conventional, monolithic medical approach.
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Background: Lung fibroblasts are implicated in abnormal tissue repair in chronic obstructive pulmonary disease (COPD). The exact mechanisms are unknown and comprehensive analysis comparing COPD- and control fibroblasts is lacking. Aim: To gain insight in the role of lung fibroblasts in COPD pathology using unbiased proteomic and transcriptomic analysis. Methods: Protein and RNA was isolated from cultured parenchymal lung fibroblasts of 17 stage IV COPD patients and 16 non-COPD controls. Proteins were analyzed using LC-MS/MS and RNA through RNA sequencing. Differential protein and gene expression in COPD was assessed via linear regression, followed by pathway enrichment, correlation analysis and immunohistological staining in lung tissue. Proteomic and transcriptomic data was compared to investigate the overlap and correlation between both levels of data. Results: We identified 40 differentially expressed (DE) proteins and zero DE genes between COPD and control fibroblasts. The most significant DE proteins were HNRNPA2B1 and FHL1. Thirteen of the 40 proteins were previously associated with COPD, including FHL1 and GSTP1. Six of the 40 proteins were related to telomere maintenance pathways, and were positively correlated with the senescence marker LMNB1. No significant correlation between gene and protein expression was observed for the 40 proteins. Conclusions: The 40 DE proteins in COPD fibroblasts include previously described COPD proteins (FHL1, GSTP1) and new COPD research targets like HNRNPA2B1. Lack of overlap and correlation between gene and protein data supports the use of unbiased proteomics analysis and indicates that different types of information are generated with both methods.
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Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings.
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Rioolwaterzuiveringen zijn de belangrijkste bron van geneesmiddelen en kunstmatige zoetstoffen in oppervlaktewater. De mate waarin rwzi’s deze organische microverontreinigingen verwijderen, lijkt te variëren van locatie tot locatie en/of in de tijd. Oriënterend onderzoek bij zeven rwzi’s in Groningen en Drenthe toonde aan dat de verwijdering van de zoetstof acesulfaam erg varieerde. Om het verschil in de biologische verwijderingscapaciteit voor acesulfaam en geneesmiddelen te kunnen verklaren, bieden nieuwe DNA-technieken wellicht uitkomst. Met Next Generation Sequencing (NGS) komen verschillen tussen bacteriepopulaties aan het licht die mogelijk verschillen in verwijdering van geneesmiddelen en zoetstoffen kunnen verklaren.
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Lichamelijke zwakte is een belangrijk onderdeel van kwetsbaarheid en komt veel voor bij oudere volwassenen. Terwijl vrouwen een hogere prevalentie en een eerder begin van kwetsbaarheid kennen zijn sekseverschillen in de ontwikkeling van lichamelijke zwakte nauwelijks bestudeerd. Daarom hebben we in spieren de veranderingen onderzocht die onderscheid maken tussen fitte en zwakke ouderen voor elk geslacht afzonderlijk. Mannen (n = 28) en vrouwen (n = 26) van 75 jaar en ouder werden gegroepeerd op basis van hun fysieke prestatiecriteria. Er werd gebruik gemaakt van spierbiopten genomen uit de vastus lateralis-spier voor genexpressie- en histologisch onderzoek. Er werden paarsgewijze vergelijkingen gemaakt tussen de sterkste en de zwakste groepen voor elk geslacht afzonderlijk, en potentiële geslachts-specifieke effecten werden beoordeeld. Zwakke vrouwen toonden een hogere expressie van ontstekingsroutes, infiltratie van NOX2-immuuncellen, samen met een hogere VCAM1-expressie. Zwakke mannen werden gekenmerkt door een kleinere diameter van type 2 (snelle) spiervezels en lagere expressie van PRKN. Zwakte-geassocieerde genexpressie-veranderingen in de spieren waren verschillend van veroudering-geassocieerde genexpressie-veranderingen, wat erop wijst dat de pathofysiologie van fysieke zwakte niet noodzakelijkerwijs afhankelijk is van veroudering. We concluderen dat zwakte-geassocieerde veranderingen in de spieren sekse-specifiek zijn. Aanbevolen wordt om bij onderzoek naar kwetsbaarheid rekening te houden met sekseverschillen, omdat deze verschillen een grote impact kunnen hebben over de ontwikkeling van (farmaceutische) interventies tegen kwetsbaarheid.
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We tested the hypothesis that in human ageing a decreased intramuscular acylcarnitine status is associated with (pre-)frailty, reduced physical performance and altered mitochondrial function. Results showed that intramuscular total carnitine levels and acetylcarnitine levels were lower in (pre-)frail old females compared to fit old females and young females, whereas no differences were observed in males. The low intramuscular acetylcarnitine levels in females correlated with low physical performance, even after correction for muscle mass (%), and were accompanied with lowered expression of genes involved in mitochondrial energy production and functionality. We concluded that in (pre-)frail old females, intramuscular total carnitine levels and acetylcarnitine levels are decreased, and this decrease is associated with reduced physical performance and low expression of a wide range of genes critical for mitochondrial function. The results stress the importance of taking sex differences into account in ageing research.
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Infographic van het project MycoEiwit: microbiële eiwit opbrengst groter op reststromen.
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The Green Biotechnology research group focusses on the application of molecular breeding/biotechnological tools and also on the development/analysis of new tools, for the breeding of enhanced vegetable crops and ornamental plants. The research group is positioned within Inholland University of Applied Sciences, Life Sciences & Chemistry and serves as a link between the breeding companies and our education of the skilled technicians of tomorrow. We are working on the development of a method for targeted mutagenesis of plant genomes using the bacterial CRISPR-Cas system. This method greatly enhances the effectiveness and speed by which new crops and plants can be developed
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