Deriving shape-based features for C. elegans locomotion using dimensionality reduction methods

High-throughput analysis of animal behavior is increasingly common following the advances of recording technology, leading to large high-dimensional data sets. This dimensionality can sometimes be reduced while still retaining relevant information. In the case of the nematode worm Caenorhabditis elegans, more than 90% of the shape variance can be captured using just four principal components. However, it remains unclear if other methods can achieve a more compact representation or contribute further biological insight to worm locomotion. Here we take a data-driven approach to worm shape analysis using independent component analysis (ICA), non-negative matrix factorization (NMF), a cosine series, and jPCA (a dynamic variant of principal component analysis [PCA]) and confirm that the dimensionality of worm shape space is close to four. Projecting worm shapes onto the bases derived using each method gives interpretable features ranging from head movements to tail oscillation. We use these as a comparison method to find differences between the wild type N2 worms and various mutants. For example, we find that the neuropeptide mutant nlp-1(ok1469) has an exaggerated head movement suggesting a mode of action for the previously described increased turning rate. The different bases provide complementary views of worm behavior and we expect that closer examination of the time series of projected amplitudes will lead to new results in the future

Visual Responses in Mice Lacking Critical Components of All Known Retinal Phototransduction Cascades

The mammalian visual system relies upon light detection by outer-retinal rod/cone photoreceptors and melanopsin-expressing retinal ganglion cells. Gnat1(-/-); Cnga3(-/-); Opn4(-/-) mice lack critical elements of each of these photoreceptive mechanisms via targeted disruption of genes encoding rod alpha transducin (Gnat1); the cone-specific alpha 3 cyclic nucleotide gated channel subunit (Cnga3); and melanopsin (Opn4). Although assumed blind, we show here that these mice retain sufficiently widespread retinal photoreception to drive a reproducible flash electroretinogram (ERG). The threshold sensitivity of this ERG is similar to that of cone-based responses, however it is lost under light adapted conditions. Its spectral efficiency is consistent with that of rod opsin, but not cone opsins or melanopsin, indicating that it originates with light absorption by the rod pigment. The TKO light response survives intravitreal injection of U73122 (a phospholipase C antagonist), but is inhibited by a missense mutation of cone alpha transducin (Gnat2(cpfl3)), suggesting Gnat2-dependence. Visual responses in TKO mice extend beyond the retina to encompass the lateral margins of the lateral geniculate nucleus and components of the visual cortex. Our data thus suggest that a Gnat1-independent phototransduction mechanism downstream of rod opsin can support relatively widespread responses in the mammalian visual system. This anomalous rod opsin-based vision should be considered in experiments relying upon Gnat1 knockout to silence rod phototransduction

Predicting path from undulations for C. elegans using linear and nonlinear resistive force theory

A basic issue in the physics of behaviour is the mechanical relationship between an animal and its s urroundings. The nematode and model organism C. elegans provides an excellent platform to explore this relationship due to its anatom ical simplicity. Nonetheless , the physics of nematode crawling, in which the worm undulates its body to move on a wet sur face, is not completely understood and the mathematical models often used to describe this phenomenon are empirical . We confirm that linear resistive force theory , one such empirical model, is effective at predicting a worm’s path from its sequence of bod y postures for forward crawling, reversing, and turning and for a broad range of different behavioural phenotypes observed in mutant worms. However, agreement between the predicted and observ ed path is lost when using this model with recently measured val ue s of the drag anisotropy. A recently proposed nonlinear extension of the resistive force theory model also provides accurate predictions, but does not resolve the discrepancy between the parameters required to achieve good path prediction and the experi mentally measured parameters. This means that while we have good effective models of worm crawling that can be used in application s such as whole - animal simulations and advance d tracking algorithms, there are still unanswered questions about the precise n ature of the physical interaction between worms and their most commonly studied laboratory substrate

Powerful and interpretable behavioural features for quantitative phenotyping of C. elegans

Behaviour is a sensitive and integrative readout of nervous system function and therefore an attractive measure for assessing the effects of mutation or drug treatment on animals. Video data provide a rich but high-dimensional representation of behaviour, and so the first step of analysis is often some form of tracking and feature extraction to reduce dimensionality while maintaining relevant information. Modern machine-learning methods are powerful but notoriously difficult to interpret, while handcrafted features are interpretable but do not always perform as well. Here, we report a new set of handcrafted features to compactly quantify Caenorhabditis elegans behaviour. The features are designed to be interpretable but to capture as much of the phenotypic differences between worms as possible. We show that the full feature set is more powerful than a previously defined feature set in classifying mutant strains. We then use a combination of automated and manual feature selection to define a core set of interpretable features that still provides sufficient power to detect behavioural differences between mutant strains and the wild-type. Finally, we apply the new features to detect time-resolved behavioural differences in a series of optogenetic experiments targeting different neural subsets

Widespread, routine occurrence of pharmaceuticals in sewage effluent, combined sewer overflows and receiving waters

Research addressing the occurrence, fate and effects of pharmaceuticals in the aquatic environment has expanded rapidly over the past two decades, primarily due to the development of improved chemical analysis methods. Significant research gaps still remain, however, including a lack of longer term, repeated monitoring of rivers, determination of temporal and spatial changes in pharmaceutical concentrations, and inputs from sources other than wastewater treatment plants (WWTPs), such as combined sewer overflows (CSOs). In addressing these gaps it was found that the five pharmaceuticals studied were routinely (51-94 % of the time) present in effluents and receiving waters at concentrations ranging from single ng to μg L-1. Mean concentrations were in the tens to hundreds ng L-1 range and CSOs appear to be a significant source of pharmaceuticals to water courses in addition to WWTPs. Receiving water concentrations varied throughout the day although there were no pronounced peaks at particular times. Similarly, concentrations varied throughout the year although no consistent patterns were observed. No dissipation of the study compounds was found over a 5 km length of river despite no other known inputs to the river. In conclusion, pharmaceuticals are routinely present in semi-rural and urban rivers and require management alongside more traditional pollutants

Chaos in the Gauge/Gravity Correspondence

We study the motion of a string in the background of the Schwarzschild black hole in AdS_5 by applying the standard arsenal of dynamical systems. Our description of the phase space includes: the power spectrum, the largest Lyapunov exponent, Poincare sections and basins of attractions. We find convincing evidence that the motion is chaotic. We discuss the implications of some of the quantities associated with chaotic systems for aspects of the gauge/gravity correspondence. In particular, we suggest some potential relevance for the information loss paradox.Comment: 29 pages, 11 figure

Palliative care for children with complex cardiac conditions: survey results.

OBJECTIVE: To explore perspectives of paediatric cardiac and palliative care professionals on providing palliative care to children with complex cardiac conditions. DESIGN: A national survey including closed-ended and open-ended questions as well as clinical scenarios designed to capture referral practices, attitudes towards palliative care, confidence delivering key components of palliative care and perspectives on for whom to provide palliative care. Responses to closed-ended questions and scenarios were analysed using descriptive statistics. Open-ended responses were analysed thematically. PARTICIPANTS: Paediatric cardiac and palliative care professionals caring for children with complex cardiac conditions in the UK. RESULTS: 177 professionals (91 cardiac care and 86 palliative care) responded. Aspects of advance care planning were the most common reasons for referral to palliative care. Palliative care professionals reported greater confidence than cardiac colleagues with such discussions. Clinicians agreed that children with no further surgical management options, comorbid genetic disorders, antenatal diagnosis of a single ventricle, ventricular device in situ, symptomatic heart failure and those awaiting heart transplantation would benefit from palliative care involvement. CONCLUSIONS: Components of palliative care, such as advance care planning, can be provided by cardiac care professionals alongside the disease-directed care of children with complex cardiac conditions. Further research and training are needed to address confidence levels in cardiac care professionals in delivering components of palliative care as well as clarification of professional roles and parent preferences in delivery of family-centred care for children with complex cardiac conditions

Regulation of neutrophilic inflammation by proteinase-activated receptor 1 during bacterial pulmonary infection

Neutrophils are key effector cells of the innate immune response to pathogenic bacteria, but excessive neutrophilic inflammation can be associated with bystander tissue damage. The mechanisms responsible for neutrophil recruitment to the lungs during bacterial pneumonia are poorly defined. In this study, we focus on the potential role of the major high-affinity thrombin receptor, proteinase-activated receptor 1 (PAR-1), during the development of pneumonia to the common lung pathogen Streptococcus pneumoniae. Our studies demonstrate that neutrophils were indispensable for controlling S. pneumoniae outgrowth but contributed to alveolar barrier disruption. We further report that intra-alveolar coagulation (bronchoalveolar lavage fluid thrombin-antithrombin complex levels) and PAR-1 immunostaining were increased in this model of bacterial lung infection. Functional studies using the most clinically advanced PAR-1 antagonist, SCH530348, revealed a key contribution for PAR-1 signaling in influencing neutrophil recruitment to lung airspaces in response to both an invasive and noninvasive strain of S. pneumoniae (D39 and EF3030) but that PAR-1 antagonism did not impair the ability of the host to control bacterial outgrowth. PAR-1 antagonist treatment significantly decreased pulmonary levels of IL-1β, CXCL1, CCL2, and CCL7 and attenuated alveolar leak. Ab neutralization studies further demonstrated a nonredundant role for IL-1β, CXCL1, and CCL7 in mediating neutrophil recruitment in response to S. pneumoniae infection. Taken together, these data demonstrate a key role for PAR-1 during S. pneumoniae lung infection that is mediated, at least in part, by influencing multiple downstream inflammatory mediators

ICAM-1 and ICAM-2 Are Differentially Expressed and Up-Regulated on Inflamed Pulmonary Epithelium, but Neither ICAM-2 nor LFA-1: ICAM-1 Are Required for Neutrophil Migration Into the Airways In Vivo

Neutrophil migration into the airways is an important process to fight infection and is mediated by cell adhesion molecules. The intercellular adhesion molecules, ICAM-1 (CD54) and ICAM-2 (CD102) are known ligands for the neutrophil integrins, lymphocyte function associated antigen (LFA)-1 (αLβ2; CD11a/CD18), and macrophage-1 antigen (Mac-1;αMβ2;CD11b/CD18) and are implicated in leukocyte migration into the lung. However, it is ill-defined how neutrophils exit the lung and the role for ICAMs in trans-epithelial migration (TEpM) across the bronchial or alveolar epithelium. We found that human and murine alveolar epithelium expressed ICAM-1, whilst the bronchial epithelium expressed ICAM-2, and both were up-regulated during inflammatory stimulation in vitro and in inflammatory lung diseases such as cystic fibrosis. Although β2 integrins interacting with ICAM-1 and -2 mediated neutrophil migration across human bronchial epithelium in vitro, neither ICAM-2 nor LFA-1 binding of ICAM-1 mediated murine neutrophil migration into the lung or broncho-alveolar space during LPS-induced inflammation in vivo. Furthermore, TEpM of neutrophils themselves resulted in increased epithelial junctional permeability and reduced barrier function in vitro. This suggests that although β2 integrins interacting with ICAMs may regulate low levels of neutrophil traffic in healthy lung or early in inflammation when the epithelial barrier is intact; these interactions may be redundant later in inflammation when epithelial junctions are disrupted and no longer limit TEpM

Receptor protein tyrosine phosphatases control Purkinje neuron firing

Spinocerebellar ataxias (SCA) are a genetically heterogeneous family of cerebellar neurodegenerative diseases characterized by abnormal firing of Purkinje neurons and degeneration. We recently demonstrated the slowed firing rates seen in several SCAs share a common etiology of hyper-activation of the Src family of non-receptor tyrosine kinases (SFKs). However, the lack of clinically available neuroactive SFK inhibitors lead us to investigate alternative mechanisms to modulate SFK activity. Previous studies demonstrate that SFK activity can be enhanced by the removal of inhibitory phospho-marks by receptor-protein-tyrosine phosphatases (RPTPs). In this Extra View we show that MTSS1 inhibits SFK activity through the binding and inhibition of a subset of the RPTP family members, and lowering RPTP activity in cerebellar slices with peptide inhibitors increases the suppressed Purkinje neuron basal firing rates seen in two different SCA models. Together these results identify RPTPs as novel effectors of Purkinje neuron basal firing, extending the MTSS1/SFK regulatory circuit we previously described and expanding the therapeutic targets for SCA patients