Amplitude and frequency modulation control of sound production in a mechanical model of the avian syrinx

Birdsong has developed into one of the important models for motor control of learned behaviour and shows many parallels with speech acquisition in humans. However, there are several experimental limitations to studying the vocal organ – the syrinx – in vivo. The multidisciplinary approach of combining experimental data and mathematical modelling has greatly improved the understanding of neural control and peripheral motor dynamics of sound generation in birds. Here, we present a simple mechanical model of the syrinx that facilitates detailed study of vibrations and sound production. Our model resembles the `starling resistor', a collapsible tube model, and consists of a tube with a single membrane in its casing, suspended in an external pressure chamber and driven by various pressure patterns. With this design, we can separately control `bronchial' pressure and tension in the oscillating membrane and generate a wide variety of `syllables' with simple sweeps of the control parameters. We show that the membrane exhibits high frequency, self-sustained oscillations in the audio range (>600 Hz fundamental frequency) using laser Doppler vibrometry, and systematically explore the conditions for sound production of the model in its control space. The fundamental frequency of the sound increases with tension in three membranes with different stiffness and mass. The lower-bound fundamental frequency increases with membrane mass. The membrane vibrations are strongly coupled to the resonance properties of the distal tube, most likely because of its reflective properties to sound waves. Our model is a gross simplification of the complex morphology found in birds, and more closely resembles mathematical models of the syrinx. Our results confirm several assumptions underlying existing mathematical models in a complex geometr

Automated visual tracking for studying the ontogeny of zebrafish swimming

The zebrafish Danio rerio is a widely used model organism in studies of genetics, developmental biology, and recently, biomechanics. In order to quantify changes in swimming during all stages of development, we have developed a visual tracking system that estimates the posture of fish. Our current approach assumes planar motion of the fish, given image sequences taken from a top view. An accurate geometric fish model is automatically designed and fit to the images at each time frame. Our approach works across a range of fish shapes and sizes and is therefore well suited for studying the ontogeny of fish swimming, while also being robust to common environmental occlusions. Our current analysis focuses on measuring the influence of vertebra development on the swimming capabilities of zebrafish. We examine wild-type zebrafish and mutants with stiff vertebrae (stocksteif) and quantify their body kinematics as a function of their development from larvae to adult (mutants made available by the Hubrecht laboratory, The Netherlands). By tracking the fish, we are able to measure the curvature and net acceleration along the body that result from the fish's body wave. Here, we demonstrate the capabilities of the tracking system for the escape response of wild-type zebrafish and stocksteif mutant zebrafish. The response was filmed with a digital high-speed camera at 1500 frames s–1. Our approach enables biomechanists and ethologists to process much larger datasets than possible at present. Our automated tracking scheme can therefore accelerate insight in the swimming behavior of many species of (developing) fish

Predicting the effects of spatiotemporal modifications of muscle activation on the tentacle extension in squid

Squid use eight arms and two slender tentacles to capture prey. The muscular stalks of the tentacles are elongated approximately 80% in 20–40 ms towards the prey, which is adhered to the terminal clubs by arrays of suckers. Using a previously developed forward dynamics model of the extension of the tentacles of the squid Doryteuthis pealeii (formerly Loligo pealeii), we predict how spatial muscle-activation patterns result in a distribution of muscular power, muscle work, and kinetic and elastic energy along the tentacle. The simulated peak extension speed of the tentacles is remarkably insensitive to delays of activation along the stalk, as well as to random variations in the activation onset. A delay along the tentacle of 50% of the extension time has only a small effect on the peak extension velocity of the tentacle compared with a zero-delay pattern. A slight delay of the distal portion relative to the proximal has a small positive effect on peak extension velocity, whereas negative delays (delay reversed along stalk) always reduce extension performance. In addition, tentacular extension is relatively insensitive to superimposed random variations in the prescribed delays along the stalk. This holds in particular for small positive delays that are similar to delays predicted from measured axonal diameters of motor neurons. This robustness against variation in the activation distribution reduces the accuracy requirements of the neuronal control and is likely due to the non-linear mechanical properties of the muscular tissue in the tentacle

Potential micro-plastics dispersal and accumulation in the North Sea, with application to the MSC Zoe incident

The fate and effects of microplastics in the marine environment are an increasingly important area of research, policy and legislation. To manage and reduce microplastics in the seas and oceans, and to help understand causes and effects, we need improved understanding of transport patterns, transit times and accumulation areas. In this paper, we use a particle tracking model to investigate the differences in dispersal and accumulation of microplastics with different properties (floating and sinking) in the North Sea. In these simulations, particles were released with a uniform horizontal distribution, and also from rivers at rates proportional to the river runoff. The results showed that floating particles can accumulate temporarily on salinity fronts and in gyres, and are deposited predominantly on west-facing beaches. Sinking particles moved more slowly and less far, accumulated in deeper areas associated with fine sediments, and were deposited more on west- and north-facing beaches. The model was also applied to the MSC Zoe incident of 1 January 2019, in which 342 containers were lost north of the Dutch Wadden islands in the southern North Sea, tracking two types of microplastics with similar properties (∼5mm floating HDPE pellets and ∼0.6mm sinking PS grains) to identify release locations and potential accumulation areas. We used field observations collected by a citizen science initiative (waddenplastic.nl) to constrain the model results. For these simulations, particles were released along the ship’s trajectory and at locations on the trajectory where debris was found. The simulations of the MSC Zoe incident showed that over 90% of floating (∼5mm) HDPE pellets beached within 3–7 weeks, and predominantly on the more eastern Dutch Wadden Islands in agreement with the field observations, and that most of the sinking (∼0.6mm) PS grains were still at sea after 6 weeks, and a large proportion may have been deposited on German shores. The work is relevant to Descriptor 10 (Marine Litter) of the EU Marine Strategy Framework Directive

Postnatal development of depth-dependent collagen density in ovine articular cartilage

<p>Abstract</p> <p>Background</p> <p>Articular cartilage (AC) is the layer of tissue that covers the articulating ends of the bones in diarthrodial joints. Adult AC is characterised by a depth-dependent composition and structure of the extracellular matrix that results in depth-dependent mechanical properties, important for the functions of adult AC. Collagen is the most abundant solid component and it affects the mechanical behaviour of AC. The current objective is to quantify the postnatal development of depth-dependent collagen density in sheep (<it>Ovis aries</it>) AC between birth and maturity. We use Fourier transform infra-red micro-spectroscopy to investigate collagen density in 48 sheep divided over ten sample points between birth (stillborn) and maturity (72 weeks). In each animal, we investigate six anatomical sites (caudal, distal and rostral locations at the medial and lateral side of the joint) in the distal metacarpus of a fore leg and a hind leg.</p> <p>Results</p> <p>Collagen density increases from birth to maturity up to our last sample point (72 weeks). Collagen density increases at the articular surface from 0.23 g/ml ± 0.06 g/ml (mean ± s.d., <it>n </it>= 48) at 0 weeks to 0.51 g/ml ± 0.10 g/ml (<it>n </it>= 46) at 72 weeks. Maximum collagen density in the deeper cartilage increases from 0.39 g/ml ± 0.08 g/ml (<it>n </it>= 48) at 0 weeks to 0.91 g/ml ± 0.13 g/ml (<it>n </it>= 46) at 72 weeks. Most collagen density profiles at 0 weeks (85%) show a valley, indicating a minimum, in collagen density near the articular surface. At 72 weeks, only 17% of the collagen density profiles show a valley in collagen density near the articular surface. The fraction of profiles with this valley stabilises at 36 weeks.</p> <p>Conclusions</p> <p>Collagen density in articular cartilage increases in postnatal life with depth-dependent variation, and does not stabilize up to 72 weeks, the last sample point in our study. We find strong evidence for a valley in collagen densities near the articular surface that is present in the youngest animals, but that has disappeared in the oldest animals. We discuss that the retardance valley (as seen with polarised light microscopy) in perinatal animals reflects a decrease in collagen density, as well as a decrease in collagen fibril anisotropy.</p

Does chytridiomycosis affect tree frog attachment?

The pandemic disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a major threat to amphibian biodiversity. For most species, the exact mechanisms of chytridiomycosis that lead to negative population dynamics remain uncertain, though mounting evidence suggests that sublethal effects could be an important driver. In this review, we propose that tree frog attachment is a promising case to study the sublethal effects of a Bd infection on amphibians. A synthesis of the current knowledge on the functional morphology of the adhesive toe pads of tree frogs, on the underlying mechanisms of tree frog attachment, and on the epidermal pathology of chytridiomycosis substantiates the hypothesis that Bd-induced epidermal alterations have the potential to disrupt tree frog attachment. We highlight a series of (biomechanical) experiments to test this hypothesis and to shed some light on the sublethal disease mechanisms of chytridiomycosis. The knowledge generated from such an approach could contribute to future research on Bd epidemiology and ultimately to the conservation of the biodiversity of arboreal anurans

Coasting in live-bearing fish: The drag penalty of being pregnant

Swimming performance of pregnant live-bearing fish is presumably constrained by the additional drag associated with the reproductive burden. Yet, it is still unclear how and to what extent the reproductive investment affects body drag of the females. We examined the effect of different levels of reproductive investment on body drag. The biggest measured increase in body volume due to pregnancy was about 43%, linked to a wetted area increase of about 16% and 69% for the frontal area. We printed three-dimensional models of live-bearing fish in a straight body posture representing different reproductive allocation (RA) levels. We measured the drag and visualized the flow around these models in a flow tunnel at different speeds. Drag grew in a power fashion with speed and exponentially with the increase of RA, thus drag penalty for becoming thicker was relatively low for low speeds compared to high ones. We show that the drag increase with increasing RA was most probably due to bigger regions of flow separation behind the enlarged belly. We suggest that the rising drag penalty with an increasing RA, possibly together with pregnancy-related negative effects on muscle- and abdominal bending performance, will reduce the maximum swimming speed

A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater

Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation of poly-contaminants in a pipeline for heavily contaminated groundwater. Groundwater moves from a polluted park to a treatment plant, where an aerated bioreactor effectively removes the contaminants. While the biomass does not settle in the reactor, sediment is collected afterwards and used to seed the new polluted groundwater via a backwash cycle. The pipeline has successfully operated since 1999, but the biological components in the reactor and the contaminated park groundwater have never been described. We sampled seven points along the pipeline, representing the entire remediation process, and characterized the changing microbial communities using genome-resolved metagenomic analysis. We assembled 297 medium- and high-quality metagenome-assembled genome sequences representing on average 46.3% of the total DNA per sample. We found that the communities cluster into two distinct groups, separating the anaerobic communities in the park groundwater from the aerobic communities inside the plant. In the park, the community is dominated by members of the genus Sulfuricurvum, while the plant is dominated by generalists from the order Burkholderiales. Known aromatic compound biodegradation pathways are four times more abundant in the plant-side communities compared to the park-side. Our findings provide a genome-resolved portrait of the microbial community in a highly effective groundwater treatment system that has treated groundwater with a complex contamination profile for two decades