Scan, extract, wrap, compute-a 3D method to analyse morphological shape differences

Distinct cell proliferation patterns underlying the development of defensive crests in Daphnia longicephala

The freshwater crustacean Daphnia is well known for its expression of morphological defenses in the presence of predators. Research into this phenomenon has mostly centered on the ecology and evolution of Daphnia defenses; information is limited on the cellular mechanisms that underlie site-specific tissue growth. We aimed to determine these cellular mechanisms, specifically those associated with the development of defensive crests in D. longicephala. With the help of a cell-proliferation assay we monitored changes in the epidermal tissue of naïve and predator-exposed D. longicephala. Based on our results, we propose that cell division is delayed in favor of cell growth, which results in crest formation. Further, we identify specific regions of proliferative activity in a time-dependent manner. Defense development starts in the ventral region, before extending in the cranial and then dorsal directions. We demonstrate that these cellular changes begin as early as 2 h after predator exposure. Our results provide new insights into the cellular processes underlying morphological defense expression in Daphnia.

Facing the Green Threat: A Water Flea's Defenses against a Carnivorous Plant

Every ecosystem shows multiple levels of species interactions, which are often difficult to isolate and to classify regarding their specific nature. For most of the observed interactions, it comes down to either competition or consumption. The modes of consumption are various and defined by the nature of the consumed organism, e.g., carnivory, herbivory, as well as the extent of the consumption, e.g., grazing, parasitism. While the majority of consumers are animals, carnivorous plants can also pose a threat to arthropods. Water fleas of the family Daphniidae are keystone species in many lentic ecosystems. As most abundant filter feeders, they link the primary production to higher trophic levels. As a response to the high predatory pressures, water fleas have evolved various inducible defenses against animal predators. Here we show the first example, to our knowledge, in Ceriodaphnia dubia of such inducible defenses of an animal against a coexisting plant predator, i.e., the carnivorous bladderwort (Utricularia x neglecta Lehm, Lentibulariaceae). When the bladderwort is present, C. dubia shows changes in morphology, life history and behavior. While the morphological and behavioral adaptations improve C. dubia's survival rate in the presence of this predator, the life-history parameters likely reflect trade-offs for the defense.

μMatch: 3D Shape Correspondence for Biological Image Data

Modern microscopy technologies allow imaging biological objects in 3D over a wide range of spatial and temporal scales, opening the way for a quantitative assessment of morphology. However, establishing a correspondence between objects to be compared, a first necessary step of most shape analysis workflows, remains challenging for soft-tissue objects without striking features allowing them to be landmarked. To address this issue, we introduce the μMatch 3D shape correspondence pipeline. μMatch implements a state-of-the-art correspondence algorithm initially developed for computer graphics and packages it in a streamlined pipeline including tools to carry out all steps from input data pre-processing to classical shape analysis routines. Importantly, μMatch does not require any landmarks on the object surface and establishes correspondence in a fully automated manner. Our open-source method is implemented in Python and can be used to process collections of objects described as triangular meshes. We quantitatively assess the validity of μMatch relying on a well-known benchmark dataset and further demonstrate its reliability by reproducing published results previously obtained through manual landmarking.

Specific Turbulence- and Chaoborus-Induced Morphotypes Affect the Streamlining Properties of Daphnia cucullata

Inducible defenses are a wide-spread defensive mechanism in Daphnia. For example, D. cucullata is known to form different adaptive morphologies under changing environmental conditions. In this species, predator presence elicits defensive helmets. Defended animals perform better and survive more frequently in predation attempts. Another peculiarity of D. cucullata is that they develop these defenses also in response to turbulence. The mechanisms that underly this defensive effect are so far unclear. Therefore, we investigated the three-dimensional morphology of the typical, the turbulence- and Chaoborus-exposed morph and analyzed their surface and volume alterations. We furthermore measured the swimming velocities of these morphs. With the determined shapes and the measured velocities, we simulated the drag force under different angles of attack and determined the energy necessary to move through the water. In the light of previous findings and hypotheses we here discuss biomechanical mechanisms that improve D. cucullata’s fitness in the investigated environments.

Thwarting predators? A three-dimensional perspective of morphological alterations in the freshwater crustacean Daphnia

Predation is a major selective agent, so that many taxa evolved phenotypically plastic defensive mechanisms. Among them are many species of the microcrustacean genus Daphnia, which respond to an increased predation risk by developing inducible morphological alterations. Some of these features are obvious and easily recognized, e.g., crests in D. longicephala, while others are rather hidden, such as the bulkier shape of D. magna induced by the presence of the tadpole shrimp Triops. In this study we investigated the extraordinary diversity of morphological adaptations in the presence of predators with different foraging strategies in six predator-prey systems. For the first time we were able to analyze the unexposed and predator-exposed morphs comprehensively using three-dimensional scanning and reconstruction. We show that morphological changes are manifold in appearance between species and predators, and go beyond what has been known from previous 2D analyses. This further demonstrates the enormous trait flexibility of Daphnia. Interestingly, we found that among this variety some species share morphological strategies to counter a predator, while others use a different strategy against the same predator. Based on these intra- and interspecific comparisons, we discuss the mechanisms by which the respective defense might operate. These data therefore contribute to a deeper understanding of the inducible defenses' morphology as well as their diversified modes of operation in Daphnia, being a cornerstone for subsequent investigations, including the determination of costs associated with morphological change.

Brain volume increase and neuronal plasticity underly predator-induced morphological defense expression in Daphnia longicephala

Predator-induced phenotypic plasticity describes the ability of prey to respond to an increased predation risk by developing adaptive phenotypes. Upon the perception of chemical predator cues, the freshwater crustacean Daphnia longicephala develops defensive crests against its predator Notonecta spec. (Heteroptera). Chemical predator perception initiates a cascade of biological reactions that leads to the development of these morphological features. Neuronal signaling is a central component in this series, however how the nervous system perceives and integrates environmental signals is not well understood. As neuronal activity is often accompanied by functional and structural plasticity of the nervous system, we hypothesized that predator perception is associated with structural and functional changes of nervous tissues. We observe structural plasticity as a volume increase of the central brain, which is independent of the total number of brain cells. In addition, we find functional plasticity in form of an increased number of inhibitory post-synaptic sites during the initial stage of defense development. Our results indicate a structural rewiring of nerve-cell connections upon predator perception and provide important insights into how the nervous system of prey species interprets predator cues and develops cost-benefit optimized defenses.

NMJ-Analyser identifies subtle early changes in mouse models of neuromuscular disease

The neuromuscular junction (NMJ) is the peripheral synapse formed between a motor neuron axon terminal and a muscle fibre. NMJs are thought to be the primary site of peripheral pathology in many neuromuscular diseases, but innervation/denervation status is often assessed qualitatively with poor systematic criteria across studies, and separately from 3D morphological structure. Here, we describe the development of ‘NMJ-Analyser’, to comprehensively screen the morphology of NMJs and their corresponding innervation status automatically. NMJ-Analyser generates 29 biologically relevant features to quantitatively define healthy and aberrant neuromuscular synapses and applies machine learning to diagnose NMJ degeneration. We validated this framework in longitudinal analyses of wildtype mice, as well as in four different neuromuscular disease models: three for amyotrophic lateral sclerosis (ALS) and one for peripheral neuropathy. We showed that structural changes at the NMJ initially occur in the nerve terminal of mutant TDP43 and FUS ALS models. Using a machine learning algorithm, healthy and aberrant neuromuscular synapses are identified with 95% accuracy, with 88% sensitivity and 97% specificity. Our results validate NMJ-Analyser as a robust platform for systematic and structural screening of NMJs, and pave the way for transferrable, and cross-comparison and high-throughput studies in neuromuscular diseases.

Higher, Faster, Better: Maternal Effects Shorten Time Lags and Increase Morphological Defenses in Daphnia lumholtzi Offspring Generations

Prey species can respond to the presence of predators by inducing phenotypic plastic traits which form morphological, life history or behavioral defenses. These so-called inducible defenses have evolved within a cost-benefit framework. They are only formed when they are needed, and costs associated with defenses are saved when predators are not present. However, a disadvantage compared to permanent defenses are lag phases between predator perception and the full formation of defenses. This may be especially important when the predation risk persists for longer periods, e.g., outlasts one generation and challenges prey offspring. We hypothesized that transgenerational induced phenotypic plasticity reduces lag phases in situations where hazards threaten specimens over several generations. We tested this in three generations of the freshwater crustacean Daphnia lumholtzi using the three-spined stickleback Gasterosteus aculeatus as predator. In the presence of chemical cues from fish D. lumholtzi expresses elongated head and tail spines. In the F0 generation defenses are constraint by a comparatively long lag phase and are not developed prior to the 3rd instar. In the F1, and F2 of induced animals this lag phase is shortened and defenses are developed upon birth. We show that induction of TGP in the mothers takes place already during the juvenile stages and transfers to the offspring generation in forms of shortened time lags and enhanced trait expression. When progeny is additionally exposed to fish cues as embryos, the addition of maternal and embryonic effects further enhances the magnitude of defense expression. Our findings detail a distinguished strategy of transgenerational phenotypic plasticity which allows to shorten lag phases of trait changes in phenotypic plasticity.

Prey capture analyses in the carnivorous aquatic waterwheel plant (Aldrovanda vesiculosa L., Droseraceae)

We investigated the predator-prey interactions between an Australian ecotype of the carnivorous waterwheel plant (Aldrovanda vesiculosa, Droseraceae) and its potential natural prey, the water flea Daphnia longicephala (Daphniidae), which also occurs in Australia. A. vesiculosa develops snap-traps, which close within ~10-100 ms after mechanical triggering by zooplankton prey. Prey capture attempts (PCAs) were recorded via high-speed cinematography in the laboratory. From 14 recorded PCAs, nine were successful for the plant (the prey was caught), and five were unsuccessful (prey could escape), resulting in a capture rate of ~64%. The prey animals' locomotion behaviour (antenna beat frequency and movement type) in trap vicinity or inside the open traps is very variable. Traps were mainly triggered with the second antennae. During trap closure, the animals moved only very little actively. A flight response in reaction to an initiated trap closure was not observed. However, several animals could escape, either by having a "lucky" starting position already outside the triggered trap, by freeing themselves after trap closure, or by being pressed out by the closing trap lobes. According to our observations in the successful PCAs, we hypothesize that the convex curvature of the two trap lobes (as seen from the outside) and the infolded trap rims are structural means supporting the capture and retention of prey. Our results are discussed in a broader biological context and promising aspects for future studies are proposed.

Automated, high-throughput measurement of size and growth curves of small organisms in well plates

Organism size and growth curves are important biological characteristics. Current methods to measure organism size, and in particular growth curves, are often resource intensive because they involve many manual steps. Here we demonstrate a method for automated, high-throughput measurements of size and growth in individual aquatic invertebrates kept in microtiter well-plates. We use a spheroid counter (Cell³iMager, cc-5000) to automatically measure size of seven different freshwater invertebrate species. Further, we generated calibration curves (linear regressions, all p < 0.0001, r² >=0.9 for Ceriodaphnoa dubia, Asellus aquaticus, Daphnia magna, Daphnia pulex; r² >=0.8 for Hyalella azteca, Chironomus spec. larvae and Culex spec. larvae) to convert size measured on the spheroid counter to traditional, microscope based, length measurements, which follow the longest orientation of the body. Finally, we demonstrate semi-automated measurement of growth curves of individual daphnids (C. dubia and D. magna) over time and find that the quality of individual growth curves varies, partly due to methodological reasons. Nevertheless, this novel method could be adopted to other species and represents a step change in experimental throughput for measuring organisms’ shape, size and growth curves. It is also a significant qualitative improvement by enabling high-throughput assessment of inter-individual variation of growth.