TY - JOUR AB - The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics. AU - Rybicki, Joel AU - Kisdi, Eva AU - Anttila, Jani ID - 43 IS - 42 JF - PNAS TI - Model of bacterial toxin-dependent pathogenesis explains infective dose VL - 115 ER - TY - JOUR AB - We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery. AU - Alderighi, Thomas AU - Malomo, Luigi AU - Giorgi, Daniela AU - Pietroni, Nico AU - Bickel, Bernd AU - Cignoni, Paolo ID - 13 IS - 4 JF - ACM Trans. Graph. TI - Metamolds: Computational design of silicone molds VL - 37 ER - TY - JOUR AB - Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli. AU - Zhang, William AU - Herde, Michel AU - Mitchell, Joshua AU - Whitfield, Jason AU - Wulff, Andreas AU - Vongsouthi, Vanessa AU - Sanchez Romero, Inmaculada AU - Gulakova, Polina AU - Minge, Daniel AU - Breithausen, Björn AU - Schoch, Susanne AU - Janovjak, Harald L AU - Jackson, Colin AU - Henneberger, Christian ID - 137 IS - 9 JF - Nature Chemical Biology TI - Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS VL - 14 ER - TY - JOUR AB - Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo. AU - Frick, Corina AU - Dettinger, Philip AU - Renkawitz, Jörg AU - Jauch, Annaïse AU - Berger, Christoph AU - Recher, Mike AU - Schroeder, Timm AU - Mehling, Matthias ID - 276 IS - 6 JF - PLoS One TI - Nano-scale microfluidics to study 3D chemotaxis at the single cell level VL - 13 ER - TY - JOUR AB - Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors. AU - Ceinos, Rosa Maria AU - Frigato, Elena AU - Pagano, Cristina AU - Frohlich, Nadine AU - Negrini, Pietro AU - Cavallari, Nicola AU - Vallone, Daniela AU - Fuselli, Silvia AU - Bertolucci, Cristiano AU - Foulkes, Nicholas S ID - 283 IS - 1 JF - Scientific Reports TI - Mutations in blind cavefish target the light regulated circadian clock gene period 2 VL - 8 ER -