171 research outputs found
Protocol to train a support vector machine for the automatic curation of bacterial cell detections in microscopy images
No full textSummary: Manual curation of bacterial cell detections in microscopy images remains a time-consuming and laborious task. This work offers a comprehensive, step-by-step tutorial on training a support vector machine to autonomously distinguish between good and bad cell detections. Jupyter notebooks are included to perform feature extraction, labeling, and training of the machine learning model. This method can readily be incorporated into profiling pipelines aimed at extracting a multitude of features across large collections of individual cells, strains, and species.For complete details on the use and execution of this protocol, please refer to Govers et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics
Conservation implications of <i>Sabellaria spinulosa</i> reef patches in a dynamic sandy-bottom environment
No full textBiogenic reefs form biodiversity hotspots and are key components of marine ecosystems, making them priority habitats for nature conservation. However, the conservation status of biogenic reefs generally depends on their size and stability. Dynamic, patchy reefs may therefore be excluded from protection. Here, we studied epibenthos and epifauna density, richness, and community composition of patchy, dynamic Sabellaria spinulosa (ross worm) reefs in the North Sea. This study was conducted by comparing boxcore (endobenthos) and video transect (epifauna) data from two research campaigns in 2017 and 2019 to the Brown Bank area on the Dutch Continental Shelf, where S. spinulosa reefs were first discovered in 2017. The Brown Bank area is characterized by dynamic, migratory bedforms at multiple scales which potentially affect biogenic reef stability. We showed that S. spinulosa habitats had a patchy distribution and alternated with habitats comprised of plain sand. Average S. spinulosa habitat patch size was 5.57 ± 0.99 m and 3.94 ± 0.22 m in 2017 and 2019 respectively (mean ± SE), which especially in 2019 closely resembled the small-scale megaripple bedforms. Contrary to the endobenthos communities that were unaffected by S. spinulosa, epifauna density and species richness were at least two times higher in S. spinulosa habitats compared to sandy habitats, resulting in different community compositions between the two habitat types. We showed that S. spinulosa persisted in the area for almost 2 years. Although the stability of individual patches remained unclear, we demonstrated that even patchy biogenic reefs may promote density and local biodiversity of mobile, epibenthic species, very likely as a result of increased habitat heterogeneity provided by reef habitat patches. This indicates that patchy biogenic reefs that occur in dynamic environments may also have high ecological value and their conservation status should be (re)considered to ensure their protection
Measuring centimeter-scale sand ripples using multibeam echosounder backscatter data from the Brown Bank area of the Dutch continental shelf
No full textBackscatter data from multibeam echosounders are commonly used to classify seafloor sediment composition. Previously, it was found that the survey azimuth affects backscatter when small organized seafloor structures, such as sand ripples, are present. These sand ripples are too small to be detected in the multibeam bathymetry. Here, we show that such azimuth effects are time dependent and are useful to examine the orientation of sand ripples in relation to the flow direction of the tide. To this end, multibeam echosounder data at four different frequencies were gathered from the area of the Brown Bank in the North Sea. The acoustic results were compared to video and tide-flow data for validation. The sand ripples affected the backscatter at all frequencies, but for the lowest frequencies the effect was spread over more beam angles. Using the acoustic data made it possible to deduce the orientations of the sand ripples over areas of multiple square kilometers. We found that the top centimeter(s) of the seafloor undergoes a complete transformation every six hours, as the orientation of the sand ripples changes with the changing tide. Our methodology allows for morphology change detection at larger scales and higher resolutions than previously achieved
The Existence and Origin of Multiple Equilibria in Sand-Mud Sediment Beds
No full textThe sediment composition of the seabed governs its mobility, hence determining sediment transport and morphological evolution of estuaries and tidal basins. Bed sediments often consist of mixtures of sand and mud, with spatial gradients in the sand/mud content. This study aims at increasing the understanding of processes driving the sediment composition in tidal basins, focusing on depositional processes. We show that bed sediments in the Wadden Sea tend to be either mud-dominated or sand-dominated, resulting in a bimodal distribution of the mud content where the two modes represent equilibrium conditions. The equilibria depend primarily on the sediment deposition fluxes, with bimodality originating from the dependence of suspended sand/mud concentrations on the local bed composition. Our analysis shows that bimodality is a phenomenon that is not only specific for the Wadden Sea; it can be expected for a wide range of suspended sediment concentrations and thus also in other systems worldwide.Coastal EngineeringEnvironmental Fluid Mechanic
Functionele fenotypische heterogeniteit in gestresseerde klonale Escherichia coli populaties
No full textWhile bacteria often become exposed to inimical conditions, the exact cellular impact and further consequences of such stressful encounters tend to remain elusive. In order to better understand bacterial inactivation and resuscitation dynamics, this dissertation ventured into quantitative live cell biology approaches to document and dissect the heterogeneous behavior within stressed bacterial populations at single-cell resolution. More specifically, using Escherichia coli as a bacterial model organism that is also representative for a number of foodborne pathogens, we focused on the effects of heat and high hydrostatic pressure stress, as well as on the management and physiological impact of protein aggregates as intracellular damage depots. Our results illustrate the potential of stress to generate a sometimes functional phenotypic heterogeneity within isogenic E. coli populations.status: Publishe
Bimodal Expression of the <i>Salmonella</i> Typhimurium <i>spv</i> Operon
No full textThe well-studied spv operon of Salmonellatyphimurium is important for causing full virulence in mice and both the regulation and function of the Spv proteins have been characterized extensively over the past several decades. Using quantitative single-cell fluorescence microscopy, we demonstrate the spv regulon to display a bimodal expression pattern that originates in the bimodal expression of the SpvR activator. The spv expression pattern is influenced by growth conditions and the specific Styphimurium strain used, but does not require Salmonella-specific virulence regulators. By monitoring real-time promoter kinetics, we reveal that SpvA has the ability to impart negative feedback on spvABCD expression without affecting spvR expression. Together, our data suggest that the SpvA protein counteracts the positive feedback loop imposed by SpvR, and could thus be responsible for dampening spvABCD expression and coordinating virulence protein production in time. The results presented here yield new insights in the intriguing regulation of the spv operon and adds this operon to the growing list of virulence factors exhibiting marked expression heterogeneity in Styphimurium.sponsorship: The authors would like to thank William Cenens, Peter Goos, Kristof Vanoirbeek, Catherine Royer, and Marjan van der Woude for helpful suggestions and fruitful discussions; Sander Van Dromme for helping to screen the Tn5-mVenus mutant library; Victor de Lorenzo for his kind gift of the pBAM1-GFP plasmid; and Johan Paulsson for his kind gift of the pDHL1029 plasmid. This work was supported by doctoral fellowships from the Flemish Agency for Innovation by Science and Technology (IWT-Vlaanderen; to I.P. and S.K.G.) and the Research Foundation - Flanders (FWO-Vlaanderen; to A.C.), and a grant from the Katholieke Universiteit Leuven Research Fund (IDO/10/012). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors declare no conflicts of interest. (Flemish Agency for Innovation by Science and Technology (IWT-Vlaanderen), Research Foundation - Flanders (FWO-Vlaanderen), Katholieke Universiteit Leuven Research Fund|IDO/10/012)status: Publishe
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