216 research outputs found
Zeekrant 2011: jaarlijkse uitgave van het Vlaams Instituut voor de Zee en de Provincie West-Vlaanderen
The influence of microgravity on invasive growth in Saccharomyces cerevisiae
This study investigates the effects of microgravity on colony growth and the morphological transition from single cells to short invasive filaments in the model eukaryotic organism Saccharomyces cerevisiae. Two-dimensional spreading of the yeast colonies grown on semi-solid agar medium was reduced under microgravity in the Sigma 1278b laboratory strain but not in the CMBSESA1 industrial strain. This was supported by the Sigma 1278b proteome map under microgravity conditions, which revealed upregulation of proteins linked to anaerobic conditions. The Sigma 1278b strain showed a reduced invasive growth in the center of the yeast colony. Bud scar distribution was slightly affected, with a switch toward more random budding. Together, microgravity conditions disturb spatially programmed budding patterns and generate strain-dependent growth differences in yeast colonies on semi-solid medium
Simple optical nanomotion method for single-bacterium viability and antibiotic response testing.
Antibiotic resistance is nowadays a major public health issue. Rapid antimicrobial susceptibility tests (AST) are one of the options to fight this deadly threat. Performing AST with single-cell sensitivity that is rapid, cheap, and widely accessible, is challenging. Recent studies demonstrated that monitoring bacterial nanomotion by using atomic force microscopy (AFM) upon exposure to antibiotics constitutes a rapid and highly efficient AST. Here, we present a nanomotion detection method based on optical microscopy for testing bacterial viability. This novel technique only requires a very basic microfluidic analysis chamber, and an optical microscope equipped with a camera or a mobile phone. No attachment of the microorganisms is needed, nor are specific bacterial stains or markers. This single-cell technique was successfully tested to obtain AST for motile, nonmotile, gram-positive, and gram-negative bacteria. The simplicity and efficiency of the method make it a game-changer in the field of rapid AST
DNA-interacting characteristics of the archaeal rudiviral protein SIRV2_Gp1
This is the final version of the article. Available from the publisher via the DOI in this record.Whereas the infection cycles of many bacterial and eukaryotic viruses have been
characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on
a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed
an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host
cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally
characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly
expressed during early stages of infection and it is the only protein that is encoded twice on the
viral genome. It harbours a helix-turn-helix motif and was therefore hypothesized to bind DNA.
The DNA-binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift
assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and
that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the
N-terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may
lead to biotechnological applications, such as the development of a toxic peptide for the containment
of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.This research was supported by the Geconcerteerde Onderzoeks Actie grant
âPhage Biosystemsâ from the KULeuven (http://www.kuleuven.be/onderzoek/kernprojecten/goa.htm). T.E.F.Q.
was supported by a FWO Pegasus Marie-Curie fellowship and a Marie-Curie Intra-European Fellowship.
The Belgian Federal Science Policy Office (Belspo) and the European Space Agency (ESA) PRODEX program
supported the work of RGW. E.P. was supported by start-up funds provided by the Vrije Universiteit Brussel (VUB)
DNAâInteracting characteristics of the archaeal Rudiviral protein SIRV2_Gp1
Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rodâshaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helixâturnâhelix motif and was therefore hypothesized to bind DNA. The DNAâbinding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the Nâterminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.Publisher PDFPeer reviewe
Machine learning method for the classification of the state of living organismsâ oscillations
The World Health Organization highlights the urgent need to address the global threat posed by antibiotic-resistant bacteria. Efficient and rapid detection of bacterial response to antibiotics and their virulence state is crucial for the effective treatment of bacterial infections. However, current methods for investigating bacterial antibiotic response and metabolic state are time-consuming and lack accuracy. To address these limitations, we propose a novel method for classifying bacterial virulence based on statistical analysis of nanomotion recordings. We demonstrated the method by classifying living Bordetella pertussis bacteria in the virulent or avirulence phase, and dead bacteria, based on their cellular nanomotion signal. Our method offers significant advantages over current approaches, as it is faster and more accurate. Additionally, its versatility allows for the analysis of cellular nanomotion in various applications beyond bacterial virulence classification
Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos
© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Naert, T., Tulkens, D., Edwards, N. A., Carron, M., Shaidani, N. I., Wlizla, M., Boel, A., Demuynck, S., Horb, M. E., Coucke, P., Willaert, A., Zorn, A. M., & Vleminckx, K. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos. Scientific Reports, 10(1), (2020): 14662, doi:10.1038/s41598-020-71412-0.CRISPR/Cas9 genome editing has revolutionized functional genomics in vertebrates. However, CRISPR/Cas9 edited F0 animals too often demonstrate variable phenotypic penetrance due to the mosaic nature of editing outcomes after double strand break (DSB) repair. Even with high efficiency levels of genome editing, phenotypes may be obscured by proportional presence of in-frame mutations that still produce functional protein. Recently, studies in cell culture systems have shown that the nature of CRISPR/Cas9-mediated mutations can be dependent on local sequence context and can be predicted by computational methods. Here, we demonstrate that similar approaches can be used to forecast CRISPR/Cas9 gene editing outcomes in Xenopus tropicalis, Xenopus laevis, and zebrafish. We show that a publicly available neural network previously trained in mouse embryonic stem cell cultures (InDelphi-mESC) is able to accurately predict CRISPR/Cas9 gene editing outcomes in early vertebrate embryos. Our observations can have direct implications for experiment design, allowing the selection of guide RNAs with predicted repair outcome signatures enriched towards frameshift mutations, allowing maximization of CRISPR/Cas9 phenotype penetrance in the F0 generation.Research in the Vleminckx laboratory is supported by the Research FoundationâFlanders (FWO-Vlaanderen) (Grants G0A1515N and G029413N), by the Belgian Science Policy (Interuniversity Attraction PolesâIAP7/07) and by the Concerted Research Actions from Ghent University (BOF15/GOA/011). Further support was obtained by the Hercules Foundation, Flanders (Grant AUGE/11/14) and the Desmoid Tumor Research Foundation and the Desmoid Tumour Foundation Canada. T.N. is funded by âKom op tegen Kankerâ (Stand up to Cancer), the Flemish cancer society and previously held PhD fellowship with VLAIO-HERMES during the course of this work. D.T. and M. C. hold a PhD fellowship from the Research Foundation-Flanders (FWO-Vlaanderen). The Zorn Lab is supported by Funding from NIH National Institute of Child Health and Human Development (NICHD) P01 HD093363. A.W. and A.B. are supported by the Ghent University (Universiteit Gent) Methusalem grant BOFMET2015000401 to Anne De Paepe. The National Xenopus Resource and Horb lab is supported by funding from the National Institutes of Health (P40 OD010997 and R01 HD084409)
Measuring Vulnerability of Marine and Coastal Habitatsâ Potential to Deliver Ecosystem Services: Complex Atlantic Region as Case Study
The main objective of this work is to promote Ecosystem Based Management (EBM), using a complex Atlantic region, to demonstrate how the InVEST model tool and associated methods can be applied to calculate benthic habitats cumulative risk and to create a vulnerability index of the potential of these habitats to deliver ecosystem services (ES). The study area, in the Western-Atlantic coast of Portugal, includes the NazarĂ© Canyon (>3,000 m depth within the study region), Ăbidos Lagoon (transitional waters), SĂŁo Martinho do Porto bay (marine inlet), and Berlengas Archipelago (UNESCO world biosphere reserve). The ES delivered by this complex coastal region supports the main regional/local socio-economic activities (e.g., fisheries and tourism activities). The approach combined the InVEST habitat risk assessment tool with the identified ES to create a proxy for the habitatsâ vulnerability to deliver ES. Within the region 28 marine benthic habitats were identified and combined with 12 classes of ES (Common International Classification of ES), and two prospective scenarios were analyzed (a potential socio-economic scenario for 2025 and a climate change scenario for the end of the century). The results show that the applied vulnerability approach enables the combination of information from different sources, including local knowledge, and the translation of the generated information into 2D spatial explicit maps that can support strategic management options, namely in the context of maritime spatial planning and âBlue Growth.â The interpretation of the habitat vulnerability approach requires the consideration of data spatial resolution, its quality, and the impact of associated pressures. However, despite the limitations and assumptions (e.g., all ES classes are equally important), models such as this have opened new avenues contributing to improve EBM, by combining spatial explicit GIS tools with supply and demand of marine ES, human activities, and their related positive and negative impacts
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