Organizational Scale Research Articles

Stable Isotope Trajectory Analysis (SITA): A new approach to quantify and visualize dynamics in stable isotope studies

AbstractEcologists working with stable isotopes have to deal with complex datasets including temporal and spatial replication, which makes the analysis and the representation of patterns of change challenging, especially at high resolution. Due to the lack of a commonly accepted conceptual framework in stable isotope ecology, the analysis and the graphical representation of stable isotope spatial and temporal dynamics of stable isotope value at the organism or community scale remained in the past often descriptive and qualitative, impeding the quantitative detection of relevant functional patterns. The recent community trajectory analysis (CTA) framework provides more explicit perspectives for the analysis and the visualization of ecological trajectories. Building on CTA, we developed the Stable Isotope Trajectory Analysis (SITA) framework, to analyze the geometric properties of stable isotope trajectories on n‐dimensional (n ≥ 2) spaces of analysis defined analogously to the traditional multivariate spaces (Ω) used in community ecology. This approach provides new perspectives into the quantitative analysis of spatio‐temporal trajectories in stable isotope spaces (Ωδ) and derived structural and functional dynamics (Ωγ space). SITA allows the calculation of a set of trajectory metrics, based on either trajectory distances or directions, and new graphical representation solutions, both easily performable in an R environment. Here, we illustrate the use of our approach by reanalyzing previously published datasets from marine, terrestrial, and freshwater ecosystems. We highlight the insights provided by this new analytic framework at the individual, population, community, and ecosystems levels, and discuss applications, limitations, and development potential.

Tracing Mobile DNAs: From Molecular to Population Scales.

Transposable elements (TEs, transposons) are mobile DNAs that are prevalent in most eukaryotic genomes. In plants, their mobility has vastly contributed to genetic diversity which is essential for adaptive changes and evolution of a species. Such mobile nature of transposon has been also actively exploited in plant science research by generating genetic mutants in non-model plant systems. On the other hand, transposon mobilization can bring about detrimental effects to host genomes and they are therefore mostly silenced by the epigenetic mechanisms. TEs have been studied as major silencing targets and acted a main feature in the remarkable growth of the plant epigenetics field. Despite the importance of transposon in plant biology and biotechnology, their mobilization and the underlying mechanisms are largely left unanswered. This is mainly because of the sequence repetitiveness of transposons, which makes their detection and analyses difficult and complicated. Recently, some attempts have been made to develop new experimental methods detecting active transposons and their mobilization behavior. These techniques reveal TE mobility in various levels, including the molecular, cellular, organismal and population scales. In this review, we will highlight the novel technical approaches in the study of mobile genetic elements and discuss how these techniques impacted on the advancement of transposon research and broadened our understanding of plant genome plasticity.

Collective Behaviors of Magnetic Active Matter: Recent Progress toward Reconfigurable, Adaptive, and Multifunctional Swarming Micro/Nanorobots.

Active matter refers to the nonequilibrium system composed of interacting units that continually dissipate energy at a single-unit level and transduce it into mechanical force or motion. Such systems are ubiquitous in nature and span most of the biological scales, ranging from cytoskeleton protein polymers at the molecular level to bacterial colonies at the cellular level to swarms of insects, flocks of birds, schools of fish, and even crowds of humans on the organismal scale. The consumption of energy within systems tends to induce the self-organization of active matter as well as the spontaneous emergence of dynamic, complex, and collective states with extraordinary properties, such as adaptability, reconfigurability, taxis, and so on. The research into active matter is expected to deepen the understanding of the underlying mechanisms of how the units in living systems interact with each other and regulate the flow of energy to improve the survival efficiency, which in turn can provide valuable insights into the engineering of artificial active systems with novel and practical collective functionalities.Because of the striking similarity in collective states, a colloidal system is an emerging approach to understanding the guiding principles of the coordinated activities in living systems. Thanks to the capabilities in batch fabrication, size control, and the modulation of interactions (e.g., dipole-dipole interactions, capillary forces, electrostatic interactions, and so on), various complex collective states have been reproduced and programmed in colloidal suspension through the elaborate design of compositions and unit-unit interactions. Among the developed colloidal systems, magnetic colloids energized by alternating magnetic fields demonstrate several unique advantages, including the high-degree-of-freedom and simple modulation of the magnetic field parameters as well as the excellent compatibility of the magnetic field with many application scenarios. Therefore, magnetic active matter not only constitutes a useful platform that leads to a discovery of fascinating emergent collective behaviors but also promises enormous potential in a variety of engineering fields.In this Account, we summarize and highlight the key efforts carried out by our group and others on the investigation of the collective behavior of magnetic active matter in the past 5 years. First, we elucidate the generation mechanisms of the emergent coordinated behaviors, which are classified according to the dominating interactions among agents, that is, the magnetic dipole-dipole interaction, hydrodynamic interaction, and weak interaction. Then we illustrate the construction of magnetic active matter with a higher level of collective effects and functionalities (e.g., reconfigurability, environmental adaptability, 3D swarming, cooperative multifunctionality, and so on) via the synergistic effects between magnetic fields and other fields. Next, potential applications of magnetic active matter are discussed, which mainly focus on the exploration in revolutionizing traditional biomedical fields. Finally, an outlook of future opportunities is presented to promote the development of magnetic active matter, which facilitates a better understanding of living counterparts and the further realization of practical applications.

Polarized Dishevelled dissolution and reassembly drives embryonic axis specification in sea star oocytes

The organismal body axes that are formed during embryogenesis are intimately linked to intrinsic asymmetries established at the cellular scale in oocytes.1 However, the mechanisms that generate cellular asymmetries within the oocyte and then transduce that polarity to organismal scale body axes are poorly understood outside of select model organisms. Here, we report an axis-defining event in meiotic oocytes of the sea star Patiria miniata. Dishevelled (Dvl) is a cytoplasmic Wnt pathway effector required for axis development in diverse species,2-4 but the mechanisms governing its function and distribution remain poorly defined. Using time-lapse imaging, we find that Dvl localizes uniformly to puncta throughout the cell cortex in Prophase I-arrested oocytes but becomes enriched at the vegetal pole following meiotic resumption through a dissolution-reassembly mechanism. This process is driven by an initial disassembly phase of Dvl puncta, followed by selective reformation of Dvl assemblies at the vegetal pole. Rather than being driven by Wnt signaling, this localization behavior is coupled to meiotic cell cycle progression and influenced by Lamp1+ endosome association and Frizzled receptors pre-localized within the oocyte cortex. Our results reveal a cell cycle-linked mechanism by which maternal cellular polarity is transduced to the embryo through spatially regulated Dvl dynamics.

Squirming in density-stratified fluids

In this work, we study the axisymmetric motion of a prototypical swimming organism, a spherical squirmer, in a linearly density-stratified fluid. We assume the inertia is negligible, the stratification is weak, and the swimmer is oriented either vertically upward or downward. The swimmer acts as a settling particle or a neutrally buoyant organism depending on the relative magnitude of its density and the ambient fluid density. While the stratification reduces the speed of a settling particle, it increases (respectively, reduces) the speed of a neutrally buoyant puller (respectively, pusher). The stratification only affects the flow far from the swimmer and this far-field flow due to a settling particle (respectively, neutrally buoyant organism) at low advection of density is same as the flow due to a point-force (respectively, force-dipole) placed in a stratified fluid. The swimmer mixes the surrounding fluid. The mixing caused by a settling particle scales as the ratio of the particle size to the stratification length scale but the mixing due to a neutrally buoyant organism scales as the ratio of the buoyancy to the viscous forces. The latter mixing estimate is much larger than the previous estimate based on the force-dipole model of an organism but still negligible compared to the oceanic mixing. These results are useful to understand the stratification effects on the motility of the organism and the induced mixing.

Mechanosensitive miR-100 coordinates TGFβ and Wnt signaling in osteocytes during fluid shear stress.

Organism scale mechanical forces elicit cellular scale changes through coordinated regulation of multiple signaling pathways. The mechanisms by which cells integrate signaling to generate a unified biological response remains a major question in mechanobiology. For example, the mechanosensitive response of bone and other tissues requires coordinated signaling by the transforming growth factor beta (TGFβ) and Wnt pathways through mechanisms that are not well‐defined. Here we report a new microRNA‐dependent mechanism that mediates mechanosensitive crosstalk between TGFβ and Wnt signaling in osteocytes exposed to fluid shear stress (FSS). From 60 mechanosensitive microRNA (miRs) identified by small‐RNAseq, miR100 expression is suppressed by in vivo hindlimb loading in the murine tibia and by cellular scale FSS in OCY454 cells. Though FSS activates both TGFβ and Wnt signaling in osteocytes, only TGFβ represses miR‐100 expression. miR‐100, in turn, antagonizes Wnt signaling by targeting and inhibiting expression of Frizzled receptors (FZD5/FZD8). Accordingly, miR‐100 inhibition blunts FSS‐ and TGFβ‐inducible Wnt signaling. Therefore, our results identify FSS‐responsive miRNAs in osteocytes, including one that integrates the mechanosensitive function of two essential signaling pathways in the osteoanabolic response of bone to mechanical load.

Early Response to Dehydration Six-Like Transporter Family: Early Origin in Streptophytes and Evolution in Land Plants.

Carbon management by plants involves the activity of many sugar transporters, which play roles in sugar subcellular partitioning and reallocation at the whole organism scale. Among these transporters, the early response to dehydration six-like (ESL) monosaccharide transporters (MSTs) are still poorly characterized although they represent one of the largest sugar transporter subfamilies. In this study, we used an evolutionary genomic approach to infer the evolutionary history of this multigenic family. No ESL could be identified in the genomes of rhodophytes, chlorophytes, and the brown algae Ectocarpus siliculosus, whereas one ESL was identified in the genome of Klebsormidium nitens providing evidence for the early emergence of these transporters in Streptophytes. A phylogenetic analysis using the 519 putative ESL proteins identified in the genomes of 47 Embryophyta species and being representative of the plant kingdom has revealed that ESL protein sequences can be divided into three major groups. The first and second groups originated in the common ancestor of all spermaphytes [ζ: 340 million years ago (MYA)] and of angiosperms (ε: 170–235 MYA), respectively, and the third group originated before the divergence of rosids and asterids (γ/1R: 117 MYA). In some eudicots (Vitales, Malpighiales, Myrtales, Sapindales, Brassicales, Malvales, and Solanales), the ESL family presents remarkable expansions of gene copies associated with tandem duplications. The analysis of non-synonymous and synonymous substitutions for the dN/dS ratio of the ESL copies of the genus Arabidopsis has revealed that ESL genes are evolved under a purifying selection even though the progressive increase of dN/dS ratios in the three groups suggests subdiversification phenomena. To further explore the possible acquisition of novel functions by ESL MSTs, we identified the gene structure and promoter cis-acting elements for Arabidopsis thaliana ESL genes. The expression profiling of Arabidopsis ESL unraveled some gene copies that are almost constitutively expressed, whereas other gene copies display organ-preferential expression patterns. This study provides an evolving framework to better understand the roles of ESL transporters in plant development and response to environmental constraints.

Multiparameter in vivo imaging in plants using genetically encoded fluorescent indicator multiplexing.

Biological processes are highly dynamic, and during plant growth, development, and environmental interactions, they occur and influence each other on diverse spatiotemporal scales. Understanding plant physiology on an organismic scale requires analyzing biological processes from various perspectives, down to the cellular and molecular levels. Ideally, such analyses should be conducted on intact and living plant tissues. Fluorescent protein (FP)-based in vivo biosensing using genetically encoded fluorescent indicators (GEFIs) is a state-of-the-art methodology for directly monitoring cellular ion, redox, sugar, hormone, ATP and phosphatidic acid dynamics, and protein kinase activities in plants. The steadily growing number of diverse but technically compatible genetically encoded biosensors, the development of dual-reporting indicators, and recent achievements in plate-reader-based analyses now allow for GEFI multiplexing: the simultaneous recording of multiple GEFIs in a single experiment. This in turn enables in vivo multiparameter analyses: the simultaneous recording of various biological processes in living organisms. Here, we provide an update on currently established direct FP-based biosensors in plants, discuss their functional principles, and highlight important biological findings accomplished by employing various approaches of GEFI-based multiplexing. We also discuss challenges and provide advice for FP-based biosensor analyses in plants.

Synchrotron-Based Imaging Reveals the Fate of Selenium in Striped Marsh Frog Tadpoles.

Synchrotron-based X-ray fluorescence microscopy (XFM) coupled with X-ray absorption near-edge structure (XANES) imaging was used to study selenium (Se) biodistribution and speciation in Limnodynastes peronii tadpoles. Tadpoles were exposed to dissolved Se (30 μg/L) as selenite (SeIV) or selenate (SeVI) for 7 days followed by 3 days of depuration. High-resolution elemental maps revealed that Se partitioned primarily in the eyes (specifically the eye lens, iris, and retinal pigmented epithelium), digestive and excretory organs of SeIV-exposed tadpoles. Speciation analysis confirmed that the majority of accumulated Se was converted to organo-Se. Multielement analyses provided new information on Se colocalization and its impact on trace element homeostasis. New insights into the fate of Se on a whole organism scale contribute to our understanding of the mechanisms and risks associated with Se pollution.

The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken)

BackgroundAnnual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used.ResultsThe impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt.ConclusionsOur results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.

Forking paths: depicting mitosis through process-based diagramming

ABSTRACT Artist researcher Anderson shares a series of drawings developed through the experimental interdisciplinary project ‘Representing Biology as Process’. In this project Anderson and collaborators have developed a new approach to depict natural history through ‘relational process drawing’. With focus on the dynamic patterns of the processes of life and guided by principles of choreography, they draw together relationships between energy, time, movement, and environment at the molecular, cellular, and organismal scale. The drawings discussed are a kind of hybrid representation – composed to varying degrees of visual, numerical and linguistic expressions – that both provide new insights and generate new questions for future research.

Understanding Reproductive Aging in Wildlife to Improve Animal Conservation and Human Reproductive Health.

Similar to humans and laboratory animals, reproductive aging is observed in wild species-from small invertebrates to large mammals. Aging issues are also prevalent in rare and endangered species under human care as their life expectancy is longer than in the wild. The objectives of this review are to (1) present conserved as well as distinctive traits of reproductive aging in different wild animal species (2) highlight the value of comparative studies to address aging issues in conservation breeding as well as in human reproductive medicine, and (3) suggest next steps forward in that research area. From social insects to mega-vertebrates, reproductive aging studies as well as observations in the wild or in breeding centers often remain at the physiological or organismal scale (senescence) rather than at the germ cell level. Overall, multiple traits are conserved across very different species (depletion of the ovarian reserve or no decline in testicular functions), but unique features also exist (endless reproductive life or unaltered quality of germ cells). There is a broad consensus about the need to fill research gaps because many cellular and molecular processes during reproductive aging remain undescribed. More research in male aging is particularly needed across all species. Furthermore, studies on reproductive aging of target species in their natural habitat (sentinel species) are crucial to define more accurate reproductive indicators relevant to other species, including humans, sharing the same environment. Wild species can significantly contribute to our general knowledge of a crucial phenomenon and provide new approaches to extend the reproductive lifespan.

Luminescence lifetime imaging of three-dimensional biological objects.

A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.

Plankton composition of Hakaluki Haor of Moulvibazar, Bangladesh

In the present study, physicochemical and biological variables related to the water quality of Hakaluki Haor were studied. Three study stations viz. Bakshimul, Jalabeel and Dudhai were investigated because of an event of mass scale of dead fish and other aquatic organisms were reported. The stations had water depths from 2.74 - 5.13 m and Secchi Disc Transparency were 0.74 - 1.91 m. The air and water temperature among the three stations ranged from 28.2 - 30.4°C and 21.8 - 28.8°C, respectively. TDS ranged from 35 - 42 mg/l, while the electric conductivity of water showed 40 - 50 μS/cm. SRP, nitrate and SRS ranged from 10.68 - 12.32 μg/l, 0.116 - 0.122 mg/l and, 16.08 - 35.42 mg/l, respectively. The concentration of DO was very poor which ranged from 2.8 - 5.4 mg/l. In all the three studied stations, the free CO2 concentration was 0.096 mg/l. Chlorophyll-a value was moderate in all the three stations (ranged within 34.67 and 40.60 μg/l). The phaeopigment concentration was low and ranged from 1.51- 8.72 μg/l among the studied stations. Concentration of ammonia was much higher (1.03 - 1.72 mg/l) than the standard value for Bangladesh (0.5 mg/l). From this analysis, it is observed that during fish kill event the concentration of ammonia was higher with low DO content which might have resulted because of the decomposition of upper foliar parts of the rice plant due to the sudden inundation. Gross α and β counts were found to be 0.01 and 0.10 Bq/l in the Haor water at the time of fish kill. From the planktonic community, 16 phytoplanktons from green algae, 14 euglenoids, 5 diatoms, 5 dinoflagellates and 12 zooplankton species were recorded. A shift in the pH of the Haor water from acidic to alkaline might have occurred during the last 3 decades. A detailed limnological study covering the climatic seasons of Bangladesh has been recommended to be carried out for Hakaluki Haor.
 Dhaka Univ. J. Biol. Sci. 30(1): 69-78, 2021 (January)

Handling the heat: Responses of two congeneric limpet species to environmental temperature differences

Poleward migrations of coastal marine species are occurring due to anthropogenic climate change. Temperature is a known driver of species distributions, however, the specific influence of temperature responsible for ecological disruption are diverse and often species-specific. If we are to predict future impacts of climate change it is imperative we have a comprehensive understanding of the influences of temperature at the scale of individual organisms, especially for ecosystem engineer species. In this study, manipulative mesocosm experiments were conducted to explore how temperature affects limpet feeding and activity rates, and duration of tenacity ability of the foot was used to assess the impact of water temperature on biological function. Mesocosm trials and biological function analysis indicated that P. vulgata may be more eurythermal, whilst P. depressa has a higher thermal tolerance while performing simple biological functions at higher temperatures. These investigations supplement the established body of research aimed at improving the predictive power of species distribution models (SDM) used to forecast the impact of climate change by pointing to potential importance of sub-lethal effects upon behaviour and performance.

Cell Adhesions Link Subcellular Actomyosin Dynamics to Tissue Scale Force Production During Vertebrate Convergent Extension

Axis extension is a fundamental biological process that shapes multicellular organisms. The design of an animal’s body plan is encoded in the genome and execution of this program is a multiscale mechanical progression involving the coordinated movement of proteins, cells, and whole tissues. Thus, a key challenge to understanding axis extension is connecting events that occur across these various length scales. Here, we use approaches from proteomics, cell biology, and tissue biomechanics to describe how a poorly characterized cell adhesion effector, the Armadillo Repeat protein deleted in Velo-Cardio-Facial syndrome (Arvcf) catenin, controls vertebrate head-to-tail axis extension. We find that Arvcf catenin is required for axis extension within the intact organism but is not required for extension of isolated tissues. We then show that the organism scale phenotype is caused by a modest defect in force production at the tissue scale that becomes apparent when the tissue is challenged by external resistance. Finally, we show that the tissue scale force defect results from dampening of the pulsatile recruitment of cell adhesion and cytoskeletal proteins to cell membranes. These results not only provide a comprehensive understanding of Arvcf function during an essential biological process, but also provide insight into how a modest cellular scale defect in cell adhesion results in an organism scale failure of development.

Ecological engineering across organismal scales: trophic-mediated positive effects of microhabitat enhancement on fishes

Retrofitting microhabitat features is a common ecological engineering technique for enhancing biodiversity and abundance of small, epilithic organisms on artificial shorelines by providing refuge spaces and/or ameliorating abiotic conditions. These features are typically too small to be utilised as refugia by larger, highly motile consumers such as fish, but they may affect these organisms through other mechanisms. This study sought to determine whether microhabitat enhancement units alter the fish abundance, richness and assemblage composition on tropical seawalls and explores possible underlying trophic mechanisms. We created 12 experimental plots consisting of 6 enhanced plots, each with 20 microhabitat enhancement tiles, and 6 control plots without tiles on intertidal seawalls at Pulau Hantu, an offshore island south of mainland Singapore. Benthic cover and fish assemblage were surveyed within each plot using photoquadrats and underwater video cameras, respectively, from April 2018 to February 2019. We found greater abundance and species richness and distinct assemblages of fish in the enhanced plots compared to the control plots. These differences were driven largely by an increase in both abundance and richness of fish species with epibenthic-feeding strategies and were significantly associated with higher biotic cover in the enhanced plots, especially epilithic algal matrix (EAM). Our results indicate that, in addition to facilitating epilithic organisms, microhabitat enhancement can provide food resources for epibenthic-feeding fishes, increase fish biodiversity, and alter fish assemblages in tropical urbanised shorelines.

Plumage patterns: Ecological functions, evolutionary origins, and advances in quantification

AbstractBirds exhibit remarkable variation in plumage patterns, both within individual feathers and among plumage patches. Differences in the size, shape, and location of pigments and structural colors comprise important visual signals involved in mate choice, social signaling, camouflage, and many other functions. While ornithologists have studied plumage patterns for centuries, recent technological advances in digital image acquisition and processing have transformed pattern quantification methods, enabling comprehensive, detailed datasets of pattern phenotypes that were heretofore inaccessible. In this review, we synthesize recent and classic studies of plumage patterns at different evolutionary and organismal scales and discuss the various roles that plumage patterns play in avian biology. We dissect the role of plumage patches as signals within and among species. We also consider the evolutionary history of plumage patterns, including phylogenetic comparative studies and evolutionary developmental research of the genetic architecture underlying plumage patterns. We also survey an expanding toolbox of new methods that characterize and quantify the size, shape, and distribution of plumage patches. Finally, we provide a worked example to illustrate a potential workflow with dorsal plumage patterns among subspecies of the Horned Lark (Eremophila alpestris) in western North America. Studies of plumage patterning and coloration have played a prominent role in ornithology thus far, and recent methodological and conceptual advances have opened new avenues of research on the ecological functions and evolutionary origins of plumage patterns in birds.

Flow and Entrainment Mechanisms Around a Freshwater Mussel Aligned With the Incoming Flow

AbstractThe paper uses information from eddy‐resolving simulations to characterize flow and turbulence around freshwater mussels at the organism scale. The focus is on the simplest case of a partially burrowed, isolated mussel aligned with the incoming flow in an open channel. The wake structure and the capacity of the flow to displace the mussel from the bed substrate and to induce local scour around the mussel are investigated as a function of the ratio between the height of the exposed part of the mussel, h, and the total mussel height, d, and as a function of the filtration velocity ratio (VR) between the incoming channel flow velocity, U0, and the mean velocity inside the excurrent siphon, Ue. As opposed to the flow past most surface‐mounted obstacles where the bed shear stresses are reduced in the wake of the body, the capacity of the flow to induce bed erosion behind isolated mussels aligned with the flow is relatively large because of strong downwelling motions inside the horizontal separated shear layers. These flow features are associated with the formation of counterrotating base vortices of unequal coherence that induce upwash behind the mussel. The total circulation of the base vortices increases with increasing h/d and VR. Though both symmetrical and antisymmetrical shedding are observed in the wake, the antisymmetrical mode dominates, and its strength increases with increasing VR. The nondimensional streamwise force acting on the emerged part of the mussel's shell increases with increasing h/d and VR. Finally, the paper discusses the effects of varying h/d and VR on the dynamics and dilution of the jet of filtered water originating in the excurrent siphon, which is important to understand how mussels affect mixing and water quality (e.g., nutrient availability and phytoplankton concentration) in natural streams.

Multidimensional phenotyping predicts lifespan and quantifies health in Caenorhabditis elegans.

Ageing affects a wide range of phenotypes at all scales, but an objective measure of ageing remains challenging, even in simple model organisms. To measure the ageing process, we characterized the sequence of alterations of multiple phenotypes at organismal scale. Hundreds of morphological, postural, and behavioral features were extracted from high-resolution videos. Out of the 1019 features extracted, 896 are ageing biomarkers, defined as those that show a significant correlation with relative age (age divided by lifespan). We used support vector regression to predict age, remaining life and lifespan of individual C. elegans. The quality of these predictions (age R2 = 0.79; remaining life R2 = 0.77; lifespan R2 = 0.72) increased with the number of features added to the model, supporting the use of multiple features to quantify ageing. We quantified the rate of ageing as how quickly animals moved through a phenotypic space; we quantified health decline as the slope of the declining predicted remaining life. In both ageing dimensions, we found that short lived-animals aged faster than long-lived animals. In our conditions, for isogenic wild-type worms, the health decline of the individuals was scaled to their lifespan without significant deviation from the average for short- or long-lived animals.