Plants are sessile organisms that deal with their -sometimes adverse- environment in well-regulated ways. Chromatin remodeling involving SWI/SNF2-type ATPases is thought to be an important epigenetic mechanism for the regulation of gene expression in different developmental programs and for integrating these programs with the response to environmental signals. In this study, we report on the role of chromatin remodeling in Arabidopsis with respect to the variability of growth and gene expression in relationship to environmental conditions.
BACKGROUND: Prednisolone and other glucocorticoids (GCs) are potent anti-inflammatory and immunosuppressive drugs. However, prolonged use at a medium or high dose is hampered by side effects of which the metabolic side effects are most evident. Relatively little is known about their effect on gene-expression in vivo, the effect on cell subpopulations and the relation to the efficacy and side effects of GCs.AIM: To identify and compare prednisolone-induced gene signatures in CD4⁺ T lymphocytes and CD14⁺ monocytes derived from healthy volunteers and to link these signatures to underlying biological pathways involved in metabolic adverse effects.MATERIALS & METHODS: Whole-genome expression profiling was performed on CD4⁺ T lymphocytes and CD14⁺ monocytes derived from healthy volunteers treated with prednisolone. Text-mining analyses was used to link genes to pathways involved in metabolic adverse events.RESULTS: Induction of gene-expression was much stronger in CD4⁺ T lymphocytes than in CD14⁺ monocytes with respect to fold changes, but the number of truly cell-specific genes where a strong prednisolone effect in one cell type was accompanied by a total lack of prednisolone effect in the other cell type, was relatively low. Subsequently, a large set of genes was identified with a strong link to metabolic processes, for some of which the association with GCs is novel.CONCLUSION: The identified gene signatures provide new starting points for further study into GC-induced transcriptional regulation in vivo and the mechanisms underlying GC-mediated metabolic side effects.
BACKGROUND: Glucocorticoids (GCs) control expression of a large number of genes via binding to the GC receptor (GR). Transcription may be regulated either by binding of the GR dimer to DNA regulatory elements or by protein-protein interactions of GR monomers with other transcription factors. Although the type of regulation for a number of individual target genes is known, the relative contribution of both mechanisms to the regulation of the entire transcriptional program remains elusive. To study the importance of GR dimerization in the regulation of gene expression, we performed gene expression profiling of livers of prednisolone-treated wild type (WT) and mice that have lost the ability to form GR dimers (GRdim).RESULTS: The GR target genes identified in WT mice were predominantly related to glucose metabolism, the cell cycle, apoptosis and inflammation. In GRdim mice, the level of prednisolone-induced gene expression was significantly reduced compared to WT, but not completely absent. Interestingly, for a set of genes, involved in cell cycle and apoptosis processes and strongly related to Foxo3a and p53, induction by prednisolone was completely abolished in GRdim mice. In contrast, glucose metabolism-related genes were still modestly upregulated in GRdim mice upon prednisolone treatment. Finally, we identified several novel GC-inducible genes from which Fam107a, a putative histone acetyltransferase complex interacting protein, was most strongly dependent on GR dimerization.CONCLUSIONS: This study on prednisolone-induced effects in livers of WT and GRdim mice identified a number of interesting candidate genes and pathways regulated by GR dimers and sheds new light onto the complex transcriptional regulation of liver function by GCs.
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.
In the past decade additive manufacturing has gained an incredible traction in the construction industry. The field of 3D concrete printing (3DCP) has advanced significantly, leading to commercially viable housing projects. The use of concrete represents a challenge because of its environmental impact and CO2 footprint. Due to its material properties, structural capacity and ability to take on complex geometries with relative ease, concrete is and will remain for the foreseeable future a key construction material. The framework required for casting concrete, in particular non-orthogonal geometries, is in itself wasteful, not reusable, contributing to its negative environmental impact. Non-standard, complex geometries generally require the use of moulds and subsystems to be produced, leading to wasteful, material-intense manufacturing processes, with high carbon footprints. This research proposal bypasses the use of wasteful scaffolding and moulds, by exploring 3D printing with concrete on reusable substructures made of sand, clay or aggregate. Optimised material depositing strategies for 3DCP will be explored, by making use of algorithmic structural optimisation. This way, material is deposited only where structurally needed, allowing for further reduction of raw-material use. This collaboration between Neutelings Riedijk Architects, Vertico and the Architectural Design and Engineering Chair of the TU Eindhoven, investigates full-scale additive manufacturing of spatially complex 3D-concrete printed components using multi-material support systems (clay, sand and aggregates). These materials can be easily shaped multiple times into substrates with complex geometries, without generating material waste. The 3D concrete printed full-scale prototypes can be used as lightweight façade elements, screens or spatial dividers. To generate waterproof components, the cavities of the extruded lattices can be filled up with lightweight clay or cement. This process allows for the exploration of new aesthetic, creative and circular possibilities, complex geometries and new material expressions in architecture and construction, while reducing raw-material use and waste.
The global market for the industrial manufacturing of recombinant proteins (RPS) is steadily increasing and demand will keep rising in years to come. Currently, RPs are already an integral part of disease therapeutics, agriculture and the chemical industry and RP manufacturing methods rely heavily on host systems such as prokaryotes and, to a lesser extent, mammalian, yeast and plant cells. When comparing these host systems, all have their specific strengths and weaknesses and numerous challenges remain to improve protein manufacturing on an industrial scale. In this project, GLO Biotics proposes an innovative plant-based RP expression platform with the potential of significantly reducing costs and process requirements compared to the current state-of-the-art systems. Specifically, this novel concept is based on the use of coconut water as a natural, cell-free ‘protein production factory’. Coconut water in nuts aged 4-6 months is composed of free-floating cell nuclei devoid of cell walls, and it has been demonstrated these nuclei can express foreign proteins. Compared to existing platforms, the relative ease of delivering foreign protein-coding genes into this system, as well as the ease of recovery of the produced protein, potentially offers an innovative platform with great commercial attractiveness. In summary, the aim of this project is to provide a proof-of-concept for coconut water as a novel and competitive RP production platform by demonstrating the production and recovery of several commercially available RPs. To this end, GLO Biotics intends to collaborate with Zuyd University of Applied Sciences (Zuyd) and the Aachen Maastricht Institute for Biobased Materials (AMIBM) in demonstrating the potential of the ‘GLO-Conuts’ expression system. As a consortium, Zuyd and GLO Biotics will utilize their shared experience in molecular engineering and DNA vector technology and AMIBM will bring their expertise in plant-based RP production and recovery.
