To accelerate differentiation between Staphylococcus aureus and Coagulase Negative Staphylococci (CNS), this study aimed to compare six different DNA extraction methods from 2 commonly used blood culture materials, i.e. BACTEC and Bact/ALERT. Furthermore, we analyzed the effect of reduced blood culture times for detection of Staphylococci directly from blood culture material. A real-time PCR duplex assay was used to compare 6 different DNA isolation protocols on two different blood culture systems. Negative blood culture material was spiked with MRSA. Bacterial DNA was isolated with: automated extractor EasyMAG (3 protocols), automated extractor MagNA Pure LC (LC Microbiology Kit MGrade), a manual kit MolYsis Plus, and a combination between MolYsis Plus and the EasyMAG. The most optimal isolation method was used to evaluate reduced bacterial culture times. Bacterial DNA isolation with the MolYsis Plus kit in combination with the specific B protocol on the EasyMAG resulted in the most sensitive detection of S.aureus, with a detection limit of 10 CFU/ml, in Bact/ALERT material, whereas using BACTEC resulted in a detection limit of 100 CFU/ml. An initial S.aureus load of 1 CFU/ml blood can be detected after 5 hours of culture in Bact/ALERT3D by combining the sensitive isolation method and the tuf LightCycler assay.
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IL22 is an important cytokine involved in the intestinal defense mechanisms against microbiome. By using ileum-derived organoids, we show that the expression of anti-microbial peptides (AMPs) and anti-viral peptides (AVPs) can be induced by IL22. In addition, we identified a bacterial and a viral route, both leading to IL22 production by T cells, but via different pathways. Bacterial products, such as LPS, induce enterocyte-secreted SAA1, which triggers the secretion of IL6 in fibroblasts, and subsequently IL22 in T cells. This IL22 induction can then be enhanced by macrophage-derived TNFα in two ways: by enhancing the responsiveness of T cells to IL6 and by increasing the expression of IL6 by fibroblasts. Viral infections of intestinal cells induce IFNβ1 and subsequently IL7. IFNβ1 can induce the expression of IL6 in fibroblasts and the combined activity of IL6 and IL7 can then induce IL22 expression in T cells. We also show that IL22 reduces the expression of viral entry receptors (e.g. ACE2, TMPRSS2, DPP4, CD46 and TNFRSF14), increases the expression of anti-viral proteins (e.g. RSAD2, AOS, ISG20 and Mx1) and, consequently, reduces the viral infection of neighboring cells. Overall, our data indicates that IL22 contributes to the innate responses against both bacteria and viruses.
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CRISPR/Cas genome engineering unleashed a scientific revolution, but entails socio-ethical dilemmas as genetic changes might affect evolution and objections exist against genetically modified organisms. CRISPR-mediated epigenetic editing offers an alternative to reprogram gene functioning long-term, without changing the genetic sequence. Although preclinical studies indicate effective gene expression modulation, long-term effects are unpredictable. This limited understanding of epigenetics and transcription dynamics hampers straightforward applications and prevents full exploitation of epigenetic editing in biotechnological and health/medical applications.Epi-Guide-Edit will analyse existing and newly-generated screening data to predict long-term responsiveness to epigenetic editing (cancer cells, plant protoplasts). Robust rules to achieve long-term epigenetic reprogramming will be distilled based on i) responsiveness to various epigenetic effector domains targeting selected genes, ii) (epi)genetic/chromatin composition before/after editing, and iii) transcription dynamics. Sustained reprogramming will be examined in complex systems (2/3D fibroblast/immune/cancer co-cultures; tomato plants), providing insights for improving tumor/immune responses, skin care or crop breeding. The iterative optimisations of Epi-Guide-Edit rules to non-genetically reprogram eventually any gene of interest will enable exploitation of gene regulation in diverse biological models addressing major societal challenges.The optimally balanced consortium of (applied) universities, ethical and industrial experts facilitates timely socioeconomic impact. Specifically, the developed knowledge/tools will be shared with a wide-spectrum of students/teachers ensuring training of next-generation professionals. Epi-Guide-Edit will thus result in widely applicable effective epigenetic editing tools, whilst training next-generation scientists, and guiding public acceptance.
Organ-on-a-chip technology holds great promise to revolutionize pharmaceutical drug discovery and development which nowadays is a tremendously expensive and inefficient process. It will enable faster, cheaper, physiologically relevant, and more reliable (standardized) assays for biomedical science and drug testing. In particular, it is anticipated that organ-on-a-chip technology can substantially replace animal drug testing with using the by far better models of true human cells. Despite this great potential and progress in the field, the technology still lacks standardized protocols and robust chip devices, which are absolutely needed for this technology to bring the abovementioned potential to fruition. Of particular interest is heart-on-a-chip for drug and cardiotoxicity screening. There is presently no preclinical test system predicting the most important features of cardiac safety accurately and cost-effectively. The main goal of this project is to fabricate standardized, robust generic heart-on-a-chip demonstrator devices that will be validated and further optimized to generate new physiologically relevant models to study cardiotoxicity in vitro. To achieve this goal various aspects will be considered, including (i) the search for alternative chip materials to replace PDMS, (ii) inner chip surface modification and treatment (chemistry and topology), (iii) achieving 2D/3D cardiomyocyte (long term) cell culture and cellular alignment within the chip device, (iv) the possibility of integrating in-line sensors in the devices and, finally, (v) the overall chip design. The achieved standardized heart-on-a-chip technology will be adopted by pharmaceutical industry. This proposed project offers a unique opportunity for the Netherlands, and Twente in particular, which has relevant expertise, potential, and future perspective in this field as it hosts world-leading companies pioneering various core aspects of the technology that are relevant for organs-on-chips, combined with two world-leading research institutes within the University of Twente.
Implanting biocompatible materials is nothing new, 3D printing of cells and extracellular matrix is well underway so growing replacement tissues in a lab is within reach. However, certain obstacles remain: How to culture functional tissues with robust and reproducible 3D architecture? Application of support structures can aid, but what if such scaffolds obstruct functionality of the graft while having limited chance of being degraded within the recipient’s body? Bioplastics are polymers of natural origin that can be degraded enzymatically. We want to use bioplastics for production of 3D printed mesh scaffolds that support cell adhesion, proliferation, differentiation, and maturation (Fig. 1). These scaffolds are designed to be temporal and sacrificial: enzymes will be used to remove the scaffold in a tissue friendly manner prior to implantation allowing tailor made, functional and ideally ‘self-only’ grafts.
