CLIJ GPU-accelerated image processing for everyone, bioRxiv, 2019-06-09
AbstractGraphics processing units (GPU) allow image processing at unprecedented speed. We present CLIJ, a Fiji plugin enabling end-users with entry level experience in programming to benefit from GPU-accelerated image processing. Freely programmable workflows can speed up image processing in Fiji by factor 10 and more using high-end GPU hardware and on affordable mobile computers with built-in GPUs.
biorxiv bioinformatics 200-500-users 2019Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays, bioRxiv, 2019-06-09
Mucus clearance constitutes the primary defence of the respiratory system against viruses, bacteria and environmental insults [1]. This transport across the entire airway emerges from the integrated activity of thousands of multiciliated cells, each containing hundreds of cilia, which together must coordinate their spatial arrangement, alignment and motility [2, 3]. The mechanisms of fluid transport have been studied extensively at the level of an individual cilium [4, 5], collectively moving metachronal waves [6–10], and more generally the hydrodynamics of active matter [11, 12]. However, the connection between local cilia architecture and the topology of the flows they generate remains largely unexplored. Here, we image the mouse airway from the sub-cellular (nm) to the organ scales (mm), characterising quantitatively its ciliary arrangement and the generated flows. Locally we measure heterogeneity in both cilia organisation and flow structure, but across the trachea fluid transport is coherent. To examine this result, a hydrodynamic model was developed for a systematic exploration of different tissue architectures. Surprisingly, we find that disorder enhances particle clearance, whether it originates from fluctuations, heterogeneity in multiciliated cell arrangement or ciliary misalignment. This resembles elements of ‘stochastic resonance’ [13–15] in a self-assembled biological system. Taken together, our results shed light on how the microstructure of an active carpet [16, 17] determines its emergent dynamics. Furthermore, this work is also directly applicable to human airway pathologies [1], which are the third leading cause of deaths worldwide [18].
biorxiv biophysics 200-500-users 2019Light-regulated collective contractility in a multicellular choanoflagellate, bioRxiv, 2019-06-07
AbstractCollective cell contractions that generate global tissue deformations are a signature feature of animal movement and morphogenesis. Nonetheless, the ancestry of collective contractility in animals remains mysterious. While surveying the Caribbean island of Curaçao for choanoflagellates, the closest living relatives of animals, we isolated a previously undescribed species (here namedChoanoeca flexasp. nov.), that forms multicellular cup-shaped colonies. The colonies rapidly invert their curvature in response to changing light levels, which they detect through a rhodopsin-cGMP pathway. Inversion requires actomyosin-mediated apical contractility and allows alternation between feeding and swimming behavior.C. flexathus rapidly converts sensory inputs directly into multicellular contractions. In this respect, it may inform reconstructions of hypothesized animal ancestors that existed before the evolution of specialized sensory and contractile cells.One Sentence SummaryA newly described choanoflagellate species forms cup-shaped colonies that reversibly invert their curvature in response to light.
biorxiv cell-biology 200-500-users 2019On the emergence of Candida auris climate change, azoles, swamps and birds, bioRxiv, 2019-06-04
The most enigmatic aspect of the rise of Candida auris as a human pathogen is that it emerged simultaneously in three continents with each clade being genetically distinct. Although new pathogenic fungal species are described regularly, these are mostly species associated with single cases in individuals who are immunosuppressed. In this study, we used phylogenetic analysis to compare C. auris with temperature susceptibility of close relatives and use these results to argue that it may be the first example of a new fungal disease emerging from climate change with the caveat that many other factors could have contributed.
biorxiv microbiology 200-500-users 2019Multiscale activity imaging in the mammary gland reveals how oxytocin enables lactation, bioRxiv, 2019-06-03
AbstractThe mammary epithelium is indispensable for the continued survival of more than 5000 mammalian species. For some, the volume of milk ejected in a single day exceeds their entire blood volume. Here, we unveil the spatiotemporal properties of physiological signals that orchestrate milk ejection. Using quantitative, multidimensional imaging of mammary cell ensembles, we reveal how stimulus-evoked Ca2+ oscillations couple to contraction in basal epithelial cells. Moreover, we show that Ca2+-dependent contractions generate the requisite force to physically-deform the innermost layer of luminal cells, forcing them to discharge the fluid that they produced and housed. Through the collective action of thousands of these biological positive-displacement pumps, each linked to a contractile ductal network, milk is delivered into the mouth of the dependent neonate, seconds after the command.One Sentence SummaryThis study provides a window into the organization, dynamics and role of epithelial Ca2+ responses in the organ principally responsible for sustaining neonatal life in mammals.
biorxiv cell-biology 200-500-users 2019Neanderthal-Denisovan ancestors interbred with a distantly-related hominin, bioRxiv, 2019-06-02
Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors—members of a “superarchaic” population that separated from other humans about 2 mya. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (1) Denisovans also interbred with superarchaics, (2) Neanderthals and Denisovans separated early in the middle Pleistocene, (3) their ancestors endured a bottleneck of population size, and (4) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (5) Neanderthals interbred with the ancestors of modern humans.One-sentence summaryWe document the earliest known interbreeding between ancient human populations and an expansion out of Africa early in the middle Pleistocene.
biorxiv evolutionary-biology 200-500-users 2019