Organizational Scale Research Articles

Imaging Neural Architecture in Brainbow Samples.

The fluorescent protein revolution has made the light microscope the most widely used tool for studying biological structure from the single-molecule to whole organism scales. However, traditional approaches are limited in their ability to resolve components in highly complex structures, such as the brain. In recent years, this limitation has been circumvented by the development of multicolor labeling methods, termed Brainbow. Brainbow tools rely on site-specific recombinases to make stochastic "choices" between different combinations of fluorescent proteins so that structures in close proximity to one another can be resolved based on their color profile. These new approaches, however, call for more refined methods of sample preparation and imaging optimized for multispectral imaging, which are presented here. The most robust approach for generating useful Brainbow data combines immunohistology with multispectral laser scanning confocal microscopy. This chapter, therefore, focuses on this particular technique, though the imaging principle discussed here is applicable to other Brainbow approaches as well.

Force percolation of contractile active gels.

Living systems provide a paradigmatic example of active soft matter. Cells and tissues comprise viscoelastic materials that exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, an active gel of semiflexible filaments, crosslinks, and molecular motors inside cells. Although individual motors are only a few nm in size and exert minute forces of a few pN, cells spatially integrate the activity of an ensemble of motors to produce larger contractile forces (∼nN and greater) on cellular, tissue, and organismal length scales. Here we review experimental and theoretical studies on contractile active gels composed of actin filaments and myosin motors. Unlike other active soft matter systems, which tend to form ordered patterns, actin-myosin systems exhibit a generic tendency to contract. Experimental studies of reconstituted actin-myosin model systems have long suggested that a mechanical interplay between motor activity and the network's connectivity governs this contractile behavior. Recent theoretical models indicate that this interplay can be understood in terms of percolation models, extended to include effects of motor activity on the network connectivity. Based on concepts from percolation theory, we propose a state diagram that unites a large body of experimental observations. This framework provides valuable insights into the mechanisms that drive cellular shape changes and also provides design principles for synthetic active materials.

Optimized Protocol for Imaging Cleared Neural Tissues Using Light Microscopy.

Understanding physical and chemical processes at an organismal scale is a fundamental goal in biology. While science is adept at explaining biological phenomena at both molecular and cellular levels, understanding how these processes translate to organismal functions remains a challenging problem. This issue is particularly significant for the nervous system where cell signaling and synaptic activities function in the context of broad neural networks. Recent progress in tissue clearing technologies lessens the barriers that previously prevented the study of large tissue samples while maintaining molecular and cellular resolution. While these new methods open vast opportunities and exciting new questions, the logistics of analyzing cellular processes in intact tissue have to be carefully considered. In this protocol, we outline a procedure to rapidly image intact brain tissue up to thousands of cubic millimeters. This experimental pipeline involves three steps: tissue clearing, tissue imaging, and data analysis. In an attempt to streamline the process for researchers entering this field, we address important considerations for each of these stages and describe an integrated solution to image intact biological tissues. Hopefully, this optimized protocol will lower the barrier of implementing high-resolution tissue imaging and facilitate the investigations of mesoscale questions at molecular and cellular resolution.

Understanding the legacy effect of previous forage crop and tillage management on soil biology, after conversion to an arable crop rotation

The soil ecosystem provides a habitat for numerous and diverse fauna which hold a pivotal role driving decomposition and nutrient cycling. However, changing land use or management can alter population dynamics, changing soil biology within the system. The implementation of different field management can improve soil fertility, whilst natural variations in plant species growth and root system may create changes to soil structure and properties. All plant species create a legacy effect within the soil to some extent; changing the environment either physically or through remaining plant residues. An experiment investigated the hypothesis that previous forage cropping and tillage management would alter the diversity and abundance of soil fauna, after changing from a stable soil environment for three years to an annual arable crop rotation to complete a five-year rotation cycle. Four replicate plots (crop 1) of either perennial ryegrass (Lolium perenne), red clover (Trifolium pratense), white clover (Trifolium repens) or chicory (Cichorium intybus) were grown in a randomised block design (2009–2013) as the first crop, before conversion to an arable crop rotation. Spring wheat (Triticum aestivum) was established in 2013, either by conventional ploughing (CP) or direct drilling (DD); and winter barley (Hordeum vulgare) established using the same methodology the following autumn 2013 and harvested in 2014. Soil fauna abundance was sampled each year after the cereal crop was harvested, and included microfauna (nematodes), mesofauna (mites) and macrofauna (earthworms). Nematodes were found in greatest abundance in the previously ryegrass treatments, with greater numbers of bacterial feeders and herbivores (in 2013). Mesostigmata and oribatid mites had larger abundances in the ryegrass treatments, although Prostigmata were found in numbers five times higher after red clover in DD plots (in 2013); earthworms were found in significantly greater numbers in the previously white clover plots, across both cereal crops. These legacy effects began to diminish by the end of the second cereal crop in the rotation (in 2014). Tillage management also affected abundance, although these were fauna dependent, with earthworm numbers being detrimentally affected by ploughing whilst nematode abundances increased with ploughing. The combination of legacy and tillage elucidated interactions with the different groups of fauna, for example, epigeic earthworms, wireworms, and prostigmatid mites showed changes in abundance dependent on the combined effect of forage and tillage. Overall, legacy effects were found across three organism scales, highlighting the impact agricultural cultivations have across the whole soil food web.

How do plants read their own shapes?

Contents 333 I. 333 II. 334 III. 334 IV. 336 336 References 337 SUMMARY: Although the sensing of shape and deformation was historically involved in the control of animal locomotion, it is now increasingly being incorporated in developmental biology. Proprioception, the perception of the self, is particularly key to the question of the reproducibility of shapes: the many regulators of growth may lead to a large array of geometries, but shape sensing restricts these diverse outputs to a limited number of forms. Mechanistically, and in addition to geometrical feedback onto the diffusion and transport of molecular factors, we highlight the role of shape-derived mechanical stress and strain in this process. Through examples at the cell, tissue and organism scales, it appears that such mechanical feedback adds robustness to morphogenesis. Interestingly, synergies exist between shape sensing and response to external cues, such as wind and gravity. Understanding the molecular basis of proprioception is now within reach and opens up many avenues for an integrative view of development.

Union of phylogeography and landscape genetics

Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the “microgeographic races” of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography.

Woodstoich III: Integrating tools of nutritional geometry and ecological stoichiometry to advance nutrient budgeting and the prediction of consumer‐driven nutrient recycling

Within the last two decades, ecological stoichiometry (ES) and nutritional geometry (NG, also known as geometric framework for nutrition) have delivered novel insights into core questions of nutritional ecology. These two nutritionally explicit frameworks differ in the ‘nutrient currency’ used and the focus of their past research; behavioural feeding strategies in NG, mainly investigating terrestrial organisms, and trophic ecology in ES, mainly in aquatic settings. However, both NG and ES have developed in explaining patterns across various scales of biological organization. Integrating specific tools of these frameworks could advance the field of nutritional ecology by unifying theoretical and empirical approaches from the organismal to ecosystem level processes. Toward this integration, we identified 1) nutrient/element budgets as a shared concept of both frameworks that encompass nutrient intake, retention, and release, 2) response surface plots of NG as powerful tools to illustrate processes at the organismal level and 3) the concept of consumer‐driven nutrient recycling (CNR) of ES as a useful tool bridging organism and ecosystem scales. We applied response surface plots to element budget data from an ES study to show how this approach can deliver new insights at the organismal level, e.g. by showing the interplay between egestion and excretion depending simultaneously on the consumed amount of carbon and phosphorus based on variation across individuals. By integrating concepts of ES and NG to model microbial uptake and mineralization of nitrogenous wastes reported in a NG study, we also demonstrate that considering biochemically explicit mineralization rates of organic wastes can improve predictions of CNR by reducing over‐ or underestimation of mineralization depending on the quality of the consumer's diet. Our presented tools and approaches can help to bridge the organismal and ecosystem level, advancing the predictive power of studies in nutritional ecology at multiple ecological scales.

Citizen Science and the Urban Ecology of Birds and Butterflies - A Systematic Review.

Citizen science has gained widespread currency as a tool for ecological research over the past decade. However, in the discipline of urban ecology, the existing contributions and future potential of citizen science engagement, specifically in terms of knowledge gain, have not yet been comprehensively explored. Here, we present a systematic review of published work on the urban ecology of birds and butterflies in relation to their use of citizen science data between 2005 and 2014. We compared the number of studies that used citizen science data to the number of studies that could potentially have employed data derived from citizen science. The take-up rates of citizen science data were 21% and 26% for birds and butterflies respectively. Most studies that employed citizen science used volunteer-derived data as primary data, and adopted Collegial, Collaborative and Contributional engagement modes to the exclusion of Contractual and Co-created arrangements. There was no evidence that citizen science studies investigated a different organismal scale (community vs. species) compared to the urban ecology literature. For both taxa, citizen science contributions were lower than expected compared to their representation in the urban ecology literature for studies on species-environment relationships at landscape and micro-environment scales, as well as behavioural ecology in general. Other research topics that could benefit from further citizen science involvement include breeding studies and guild analyses for birds, and multi-taxa studies for butterflies. Promising models of citizen science engagement for urban ecology are highlighted in relation to their thematic foci and methodological detail, and a number of research questions that could be productively addressed using citizen science are identified. The dynamics of contemporary engagement between citizen science and urban ecology described by this review could inform the design and refinement of urban ecology–citizen science programmes in order to optimise their scientific contributions.

Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in reef corals and potential roles of epigenetics on survival and fitness in the face of global climate change.

Complementary approaches to diagnosing marine diseases: a union of the modern and the classic.

Linking marine epizootics to a specific aetiology is notoriously difficult. Recent diagnostic successes show that marine disease diagnosis requires both modern, cutting-edge technology (e.g. metagenomics, quantitative real-time PCR) and more classic methods (e.g. transect surveys, histopathology and cell culture). Here, we discuss how this combination of traditional and modern approaches is necessary for rapid and accurate identification of marine diseases, and emphasize how sole reliance on any one technology or technique may lead disease investigations astray. We present diagnostic approaches at different scales, from the macro (environment, community, population and organismal scales) to the micro (tissue, organ, cell and genomic scales). We use disease case studies from a broad range of taxa to illustrate diagnostic successes from combining traditional and modern diagnostic methods. Finally, we recognize the need for increased capacity of centralized databases, networks, data repositories and contingency plans for diagnosis and management of marine disease.

The adaptive capacity of lake food webs: from individuals to ecosystems

AbstractAquatic ecosystems support size structured food webs, wherein predator‐prey body sizes span orders of magnitude. As such, these food webs are replete with extremely generalized feeding strategies, especially among the larger bodied, higher trophic position taxa. The movement scale of aquatic organisms also generally increases with body size and trophic position. Together, these body size, mobility, and foraging relationships suggest that organisms lower in the food web generate relatively distinct energetic pathways by feeding over smaller spatial areas. Concurrently, the potential capacity for generalist foraging and spatial coupling of these pathways often increases, on average, moving up the food web toward higher trophic levels. We argue that these attributes make for a food web architecture that is inherently ‘adaptive’ in its response to environmental conditions. This is because variation in lower trophic level dynamics is dampened by the capacity of predators to flexibly alter their foraging behavior. We argue that empirical, theoretical, and applied research needs to embrace this inherently adaptive architecture if we are to understand the relationship between structure and function in the face of ongoing environmental change. Toward this goal, we discuss empirical patterns in the structure of lake food webs to suggest that ecosystems change consistently, from individual traits to the structure of whole food webs, under changing environmental conditions. We then explore an empirical example to reveal that explicitly unfolding the mechanisms that drive these adaptive responses offers insight into how human‐driven impacts, such as climate change, invasive species, and fisheries harvest, ought to influence ecosystem structure and function (e.g., stability, secondary productivity, maintenance of major energy pathways). We end by arguing that such a directed food web research program promises a powerful across‐scale framework for more effective ecosystem monitoring and management.

Organismic-Scale Remote Sensing of Canopy Foliar Traits in Lowland Tropical Forests

Airborne high fidelity imaging spectroscopy (HiFIS) holds great promise for bridging the gap between field studies of functional diversity, which are spatially limited, and satellite detection of ecosystem properties, which lacks resolution to understand within landscape dynamics. We use Carnegie Airborne Observatory HiFIS data combined with field collected foliar trait data to develop quantitative prediction models of foliar traits at the tree-crown level across over 1000 ha of humid tropical forest. We predicted foliar leaf mass per area (LMA) as well as foliar concentrations of nitrogen, phosphorus, calcium, magnesium and potassium for canopy emergent trees (R2: 0.45–0.67, relative RMSE: 11%–14%). Correlations between remotely sensed model coefficients for these foliar traits are similar to those found in laboratory studies, suggesting that the detection of these mineral nutrients is possible through their biochemical stoichiometry. Maps derived from HiFIS provide quantitative foliar trait information across a tropical forest landscape at fine spatial resolution, and along environmental gradients. Multi-nutrient maps implemented at the fine organismic scale will subsequently provide new insight to the functional biogeography and biological diversity of tropical forest ecosystems.

Representative Sinusoids for Hepatic Four-Scale Pharmacokinetics Simulations

The mammalian liver plays a key role for metabolism and detoxification of xenobiotics in the body. The corresponding biochemical processes are typically subject to spatial variations at different length scales. Zonal enzyme expression along sinusoids leads to zonated metabolization already in the healthy state. Pathological states of the liver may involve liver cells affected in a zonated manner or heterogeneously across the whole organ. This spatial heterogeneity, however, cannot be described by most computational models which usually consider the liver as a homogeneous, well-stirred organ.The goal of this article is to present a methodology to extend whole-body pharmacokinetics models by a detailed liver model, combining different modeling approaches from the literature. This approach results in an integrated four-scale model, from single cells via sinusoids and the organ to the whole organism, capable of mechanistically representing metabolization inhomogeneity in livers at different spatial scales. Moreover, the model shows circulatory mixing effects due to a delayed recirculation through the surrounding organism.To show that this approach is generally applicable for different physiological processes, we show three applications as proofs of concept, covering a range of species, compounds, and diseased states: clearance of midazolam in steatotic human livers, clearance of caffeine in mouse livers regenerating from necrosis, and a parameter study on the impact of different cell entities on insulin uptake in mouse livers.The examples illustrate how variations only discernible at the local scale influence substance distribution in the plasma at the whole-body level. In particular, our results show that simultaneously considering variations at all relevant spatial scales may be necessary to understand their impact on observations at the organism scale.

Constraint around Quarter-Power Allometric Scaling in Wild Tomatoes (Solanum sect. Lycopersicon; Solanaceae)

The West-Brown-Enquist (WBE) metabolic scaling theory posits that many organismal features scale predictably with body size because of selection to minimize transport costs in resource distribution networks. Many scaling exponents are quarter-powers, as predicted by WBE, but there are also biologically significant deviations that could reflect adaptation to different environments. A central but untested prediction of the WBE model is that wide deviation from optimal scaling is penalized, leading to a pattern of constraint on scaling exponents. Here, we demonstrate, using phylogenetic comparative methods, that variation in allometric scaling between mass and leaf area across 17 wild tomato taxa is constrained around a value indistinguishable from that predicted by WBE but significantly greater than 2/3 (geometric-similarity model). The allometric-scaling exponent was highly correlated with fecundity, water use, and drought response, suggesting that it is functionally significant and therefore could be under selective constraints. However, scaling was not strictly log-log linear but rather declined during ontogeny in all species, as has been observed in many plant species. We caution that although our results supported one prediction of the WBE model, it did not strongly test the model in other important respects. Nevertheless, phylogenetic comparative methods such as those used here are powerful but underutilized tools for metabolic ecology that complement existing methods to adjudicate between models.

A Force Balance Can Explain Local and Global Cell Movements during Early Zebrafish Development

Embryonic morphogenesis takes place via a series of dramatic collective cell movements. The mechanisms that coordinate these intricate structural transformations across an entire organism are not well understood. In this study, we used gentle mechanical deformation of developing zebrafish embryos to probe the role of physical forces in generating long-range intercellular coordination during epiboly, the process in which the blastoderm spreads over the yolk cell. Geometric distortion of the embryo resulted in nonuniform blastoderm migration and realignment of the anterior-posterior (AP) axis, as defined by the locations at which the head and tail form, toward the new long axis of the embryo and away from the initial animal-vegetal axis defined by the starting location of the blastoderm. We found that local alterations in the rate of blastoderm migration correlated with the local geometry of the embryo. Chemical disruption of the contractile ring of actin and myosin immediately vegetal to the blastoderm margin via Ca2+ reduction or treatment with blebbistatin restored uniform migration and eliminated AP axis reorientation in mechanically deformed embryos; it also resulted in cellular disorganization at the blastoderm margin. Our results support a model in which tension generated by the contractile actomyosin ring coordinates epiboly on both the organismal and cellular scales. Our observations likewise suggest that the AP axis is distinct from the initial animal-vegetal axis in zebrafish.

Multiscale modelling in immunology: a review.

One of the greatest challenges in biomedicine is to get a unified view of observations made from the molecular up to the organism scale. Towards this goal, multiscale models have been highly instrumental in contexts such as the cardiovascular field, angiogenesis, neurosciences and tumour biology. More recently, such models are becoming an increasingly important resource to address immunological questions as well. Systematic mining of the literature in multiscale modelling led us to identify three main fields of immunological applications: host-virus interactions, inflammatory diseases and their treatment and development of multiscale simulation platforms for immunological research and for educational purposes. Here, we review the current developments in these directions, which illustrate that multiscale models can consistently integrate immunological data generated at several scales, and can be used to describe and optimize therapeutic treatments of complex immune diseases.

Organismic Remote Sensing for Tropical Forest Ecology and Conservation1,2

Tropical forests are vast and scientifically underexplored places. Biotic losses, gains, and reorganization within these systems go undetected due to a lack of access to technologies needed to monitor forest cover, composition, and carbon content. Provision of forest cover-monitoring tools for non-scientists has, thus, become a focus of innovation in the remote-sensing community, while advances in high-resolution forest carbon and biodiversity mapping science has progressed more slowly. This paper focuses on high-resolution remote-sensing developments to measure and monitor tropical forest canopies at the “organismic scale,” which is the resolution that resolves individual canopies and species throughout the forest landscape. Emphasis is placed on how forest carbon stocks can be mapped with precision and accuracy comparable to that of field-based estimates. Biodiversity mapping poses the greatest challenge, but recent advances in three-dimensional functional and structural trait imaging can reveal variation in species richness, abundance, and functional diversity over large geographic regions. The pay-off in pursuing these studies will be a vastly improved understanding of tropical biodiversity patterns and their underlying ecological and evolutionary drivers, which will have positive cascading effects on conservation decision-making and resource policy development.

Metabolic insights from zebrafish genetics, physiology, and chemical biology.

Metabolic diseases—atherosclerotic cardiovascular disease, type 2 diabetes mellitus, obesity, and non-alcoholic fatty liver disease––have reached pandemic proportions. Across gene, cell, organ, organism, and social-environmental scales, fundamental discoveries of the derangements that occur in these diseases are required to develop effective new treatments. Here we will review genetic, physiological, pathological and chemical biological discoveries in the emerging zebrafish model for studying metabolism and metabolic diseases. We present a synthesis of recent studies using forward and reverse genetic tools to make new contributions to our understanding of lipid trafficking, diabetes pathogenesis and complications, and to β-cell biology. The technical and physiological advantages and the pharmacological potential of this organism for discovery and validation of metabolic disease targets are stressed by our summary of recent findings. We conclude by arguing that metabolic research using zebrafish will benefit from adoption of conventional blood and tissue metabolite measurements, employment of modern imaging techniques, and development of more rigorous metabolic flux methods.

Prevalence of dental fluorosis in school going children of Dammam, Saudi Arabia

Objective: Purpose of the study was to determine the prevalence of dental fluorosis and its pattern in primary and permanent teeth among 6-12-year-old Pakistani school going children living in Dammam, Saudi Arabia. Materials and Methods: This cross-sectional study was performed between June and September 2014. A total number of screened children were 496 among them 259 were males and 237 were females. World Health Organization's scale was used to examine children for dental fluorosis. Results: Prevalence of dental fluorosis was found to be 33% among a total number of examined children. Among the children who had dental fluorosis (n = 164), it was observed that mild and moderate level of fluorosis were prevailing in 113 (69%) children. Furthermore, a number of males who were suffering from fluorosis was more than the females. There were 97 males and 67 females found affected from dental fluorosis and this difference was found statistically significant (P = 0.038). Conclusion: Prevalence of dental fluorosis among Pakistani school going children was not high. However, the severity of fluorosis was alarming, mild, and a moderate level of fluorosis was observed in most of the children who were affected from fluorosis.

TimerQuant: A modelling approach to tandem fluorescent timer design and data interpretation for measuring protein turnover in embryos

Studies on signalling dynamics in living embryos have been limited by a scarcity of in vivo reporters. Tandem fluorescent protein timers provide a generic method for detecting changes in protein population age and thus provide readouts for signalling events that lead to changes in protein stability or location. When imaged with quantitative dual-colour fluorescence microscopy, tandem timers offer detailed ‘snapshot’ readouts of signalling activity from subcellular to organismal scales, and therefore have the potential to revolutionise studies in developing embryos. Here we use computer modelling and embryo experiments to explore the behaviour of tandem timers in developing systems. We present a mathematical model of timer kinetics and provide software tools that will allow experimentalists to select the most appropriate timer designs for their biological question, and guide interpretation of the obtained readouts. Through the generation of a series of novel zebrafish reporter lines, we confirm experimentally that our quantitative model can accurately predict different timer responses in developing embryos and explain some less expected findings. For example, increasing the FRET efficiency of a tandem timer actually increases the ability of the timer to detect differences in protein half-life. Finally, while previous studies have used timers to monitor changes in protein turnover, our model shows that timers can also be used to facilitate the monitoring of gene expression kinetics in vivo.