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86 results for “functional coordination”
Dataset and R code: Above and belowground functional trait coordination in the Neotropical understory genus Costus
<p>Dataset and R code accompanying the paper "Above and belowground functional trait coordination in the Neotropical understory genus <em>Costus</em>" published by AoB Plants. </p>
Data_Schönauer et al. (2023)_Root and branch hydraulic functioning and trait coordination across organs in drought-deciduous and evergreen tree species of a subtropical highland forest
<p>Data used in</p> <p>Schönauer, M., Hietz, P., Schuldt, B., and Rewald, B. (2023). Root and branch hydraulic functioning and trait coordination across organs in drought-deciduous and evergreen tree species of a subtropical highland forest. Frontiers in plant science 14, 1127292. doi: 10.3389/fpls.2023.1127292</p>
An information theory-based machine learning approach to detecting functionally conserved and coordinated protein dynamics
<p>The application of machine learning classification to the molecular dynamics of the functional states of protein allows for application of an information theoretic framework familiar to traditional bioinformatics. The functional states of proteins involving binding interactions with partners comprised of protein, DNA or small molecules can first be defined in a binary fashion (i.e. bound vs unbound), subsequently simulated in molecular dynamics software, and then employed as a comparative training set for a binary machine learning classifier capable of discerning the complex dynamical consequences of binding interaction. This learner can subsequently be deployed on new simulations of the functionally bound state to validate its ability to recognize the molecular motions that are supporting binding function. Regions of proteins with functionally conserved dynamics will induce significant local correlations in learning performance across independent validation runs. Through case studies of Rbp subunit 4/7 interaction in RNA Pol II and DNA-protein interactions of TATA binding protein, we demonstrate this method of detecting functionally conserved protein dynamics. We also demonstrate how Shannon information, relative entropy and mutual information can be applied to these binary classification states of dynamic simulations in order to compare dynamics and identify concerted motions involved in dynamic interactions across sites.</p>
Intraspecific functional trait variation and coordination in Schizachyrium scoparium
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Trait coordination and environmental filters shape functional trait distributions of forest understory herbs
We test the importance of environmental filtering and trait covariance for structuring the functional traits of understory herbaceous communities.
The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population
Adaptive radiations are often stereotypical, as populations repeatedly specialize along conserved environmental axes. Phenotypic plasticity may be similarly stereotypical, as individuals respond to environmental cues. These parallel patterns of variation, which are often consistent across traits, have led researchers to propose that plasticity can facilitate predictable patterns of evolution along environmental gradients. This "flexible stem" model of evolution raises questions about the genetic nature of plasticity, including: How complex is the genetic basis for plasticity? Is plasticity across traits mediated by many distinct loci, or few "global" regulators? To address these questions, we reared a hybrid cichlid mapping population on alternate diet regimes mimicking an important environmental axis. We show that plasticity across an array of ecologically relevant traits is generally morphologically integrated, such that traits respond in a coordinated manner, especially those with overlapping function. Our genetic data are more ambiguous. While our mapping experiment provides little evidence for global genetic regulators of plasticity, these data do contain a genetic signal for the integration of plasticity across traits. Overall, our data suggest a compromise between genetic modularity, whereby plasticity may evolve independently across traits, and low-level but widespread genetic integration, establishing the potential for plasticity to experience coordinated evolution.
Data from: Coordinated ARP2/3 and glycolytic activities regulate the morphological and functional fitness of human CD8+ T cells
<p>CD8<sup>+</sup> T cells rely on actin cytoskeleton remodeling to search for target cells and assemble the immunological synapse (IS) for lethal hit delivery. We here investigated how the energy expenditure related to actin remodeling might influence the fitness of human cytotoxic T cells. We first established that the spreading ability of CD8<sup>+</sup> T cells in conditions of LFA-1 and TCR engagement mirrored the cytotoxic potential of these cells. Morphological and functional fitness were both potentiated by IL-2, which co-stimulated the transcription of glycolytic enzymes, actin isoforms and the subunits of the ARP2/3 complex. This molecular program scaled with F-actin content and cell spreading. Blockade of glycolysis impaired F-actin remodeling at the lamellipodium, chemokine-driven motility and synaptic adhesion, while blockade of mitochondrial OXPHOS affected F-actin less severely and selectively reduced cell elongation during confined migration. Although T cells deficient for the ARP2/3 subunit ARPC1B increased their ATP content upon IL-2 exposure, their morphological and functional defects were only partially corrected, pointing to the pivotal position of ARP2/3 mediated actin polymerization as integrator of T cell energetic state. Our study therefore highlights that the ability of effector T cells to migrate, form IS and ultimately kill target cells depends on a tight coordination of their metabolic and actin remodeling activities.</p>
Data from: Coordinated ARP2/3 and glycolytic activities regulate the morphological and functional fitness of human CD8+ T cells
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The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population
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Data from: Weak coordination between leaf structure and function among closely related tomato species
Theory predicts that natural selection should favor coordination between leaf physiology, biochemistry and anatomical structure along a functional trait spectrum from fast, resource-acquisitive syndromes to slow, resource-conservative syndromes. However, the coordination hypothesis has rarely been tested at a phylogenetic scale most relevant for understanding rapid adaptation in the recent past or for the prediction of evolutionary trajectories in response to climate change. We used a common garden to examine genetically based coordination between leaf traits across 19 wild and cultivated tomato taxa. We found weak integration between leaf structure (e.g. leaf mass per area) and physiological function (photosynthetic rate, biochemical capacity and CO2 diffusion), even though all were arrayed in the predicted direction along a 'fast–slow' spectrum. This suggests considerable scope for unique trait combinations to evolve in response to new environments or in crop breeding. In particular, we found that partially independent variation in stomatal and mesophyll conductance may allow a plant to improve water-use efficiency without necessarily sacrificing maximum photosynthetic rates. Our study does not imply that functional trait spectra, such as the leaf economics spectrum, are unimportant, but that many important axes of variation within a taxonomic group may be unique and not generalizable to other taxa.
Supporting Information for "Tetrazole-functionalized Organoboranes Exhibiting Dynamic Intramolecular N→B-Coordination and Cyanide-selective Anion Bin"
<p>Abstract: Starting from two different cyano-functionalized organoboranes, we demonstrate that 1,3-dipolar [3+2] azide-nitrile cy-cloaddition can serve to generate libraries of alkyl-tetrazole-functionalized compounds capable of intramolecular NB-Lewis adduct formation. Due to the lower basicity of tetrazoles, structures can be generated that exhibit weak and labile NB-coordination. The reaction furnishes 1- and 2-alkylated regio-isomers that exhibit different effective Lewis-acidities at the boron centers, and vary in their optical absorption and fluorescence properties. Indeed, we identified derivatives capable of selectively binding cyanide over fluoride, as confirmed by 11B NMR. This finding demonstrates the potentialities of this synthetic strategy to systematically finetune the properties of lead structures that are of interest as chemical sensors.</p> <p>Content:</p> <ul> <li>Output filed from Computational Studies</li> <li>Raw data and Analysis from Fluorescence Titrations</li> <li>Crystal data</li> <li>ESI file in .pdf format containing experimental procedures and analytical data.</li> </ul>
Supporting Information for "Tetrazole-functionalized Organoboranes Exhibiting Dynamic Intramolecular N→B-Coordination and Cyanide-selective Anion Bin"
<p>Abstract: Starting from two different cyano-functionalized organoboranes, we demonstrate that 1,3-dipolar [3+2] azide-nitrile cy-cloaddition can serve to generate libraries of alkyl-tetrazole-functionalized compounds capable of intramolecular NB-Lewis adduct formation. Due to the lower basicity of tetrazoles, structures can be generated that exhibit weak and labile NB-coordination. The reaction furnishes 1- and 2-alkylated regio-isomers that exhibit different effective Lewis-acidities at the boron centers, and vary in their optical absorption and fluorescence properties. Indeed, we identified derivatives capable of selectively binding cyanide over fluoride, as confirmed by 11B NMR. This finding demonstrates the potentialities of this synthetic strategy to systematically finetune the properties of lead structures that are of interest as chemical sensors.</p> <p>Content:</p> <ul> <li>Output files from Computational Studies</li> <li>Raw data and Analysis from Fluorescence Titrations</li> <li>Crystal data</li> <li>ESI file in .pdf format containing experimental procedures and analytical data.</li> </ul>
Leveraging functional traits of cover crops to coordinate crop productivity and soil health
<p><span>1. Plants act as ecosystem engineers playing fundamental roles in steering their surroundings, including soil abiotic and biotic conditions, soil organisms, and the complex soil food web they comprise. Trait-based approaches have been considered a 'Holy Grail' in linking plants to ecosystem functions, but the mechanistic relationship between plant traits and the soil food web as an indicator of soil health remains poorly understood.</span></p> <p><span>2. We examined this relationship for 16 cover crop species differing in leaf and root traits in a field experiment where corn (Zea mays) was the main crop. Based on functional traits, the cover crop species were categorized into two ecological strategies at either end of the resource acquisitive-conservative spectrum. We investigated the effects of cover crop ecological strategies on corn productivity and soil health. We used soil nematodes as an indicator of soil health and analyzed soil physico-chemical properties and microbial community activities.</span></p> <p><span>3. We found that acquisitive cover crops supported higher soil resource availability, bacterial energy channels in the soil food web, and greater corn productivity than conservative cover crops. In contrast, conservative cover crops supported higher abundances of fungivores and omni-carnivores than acquisitive cover crop, which reflected a more structured and complex soil food web, implying a healthier soil ecosystem. Conservative cover crops also increased corn productivity compared to the no cover crop control treatment.</span></p> <p><span>4. Synthesis and applications. Collectively, this work shows that cover crops with distinct ecological strategies had their own strengths to enhance ecosystem functions: acquisitive and conservative cover crops improved crop productivity and soil health, respectively. These results indicates that farmers and policy makers can make trait-based choices in selecting cover crop best serving the local needs. This points to a win-win solution for food production and ecosystem sustainability.</span></p>
Data from: Grassland management regimes alter the coordination of plant functional traits and nutrient resorption in semiarid grasslands
<p>Grazing and enclosure (grazing exclusion) are the main grassland management regimes that affect nutrient cycling and ecosystem function by altering plant traits. However, the coordination among plant functional traits and nutrient resorption under different grassland management regimes remains unclear. We examined the coordination of eight root and four leaf traits along with the nitrogen (N) and phosphorus (P) resorption efficiencies under four grazing intensities and two enclosure chronosequences in a semiarid steppe ecosystem in China. The principal components analysis (PCA) of root traits and multiple factors analysis of root and leaf traits showed two-dimensional economic spaces at the individual level. Increasing grazing intensity shifts species and community trait composition from conservative to acquisitive with increases in specific root length, specific root area, root alkaline phosphatase activity, and specific leaf area, accelerating nutrient cycling and coordination among traits. Increasing grazing intensity promoted nutrient resorption efficiency. Such adaptations optimize plant nutrient acquisition and nutrient conservation under nutrient-poor conditions. Conversely, long-term enclosure increases plant nutrient and light acquisition by promoting root tissue density, mycorrhizal colonization, and specific leaf area. The conservative (e.g., <em>Stipa grandis</em>) and acquisitive species (e.g., <em>Carex korshinskyi</em>) dominated under grazing, whereas the mid-acquisitive species, including <em>Leymus chinensis</em> and <em>Agropyron cristatum</em>,<em> </em>dominated under enclosure. The observed N and P resorption efficiencies decrease with increasing PC1 score (increase in nutrient acquisition by itself) in root PCA, indicating the trade-off between nutrient-conservative and nutrient-acquisitive strategies. Community-weighted mean traits were primarily driven by intraspecific trait variation, enhancing the adaptability of plants and communities to environmental changes and external stressors. Our study highlights the coordination among above- and below-ground traits, as well as the trade-off between root nutrient acquisition and leaf nutrient resorption under different grassland management regimes in semi-arid grassland ecosystems. From these findings, we conclude that enhancing soil nutrient availability is the most effective approach to the solution to grazing-induced grassland degradation. This knowledge is crucial for devising more effective strategies for sustainable land use and biodiversity conservation in grassland ecosystems.</p>
Data from: The function of the ophiuroid nerve ring: how a decentralized nervous system controls coordinated locomotion
Echinoderms lack a centralized nervous control system yet each extant echinoderm class has evolved unique and effective strategies for locomotion. Brittle stars (Ophiuroidea) stride swiftly over the seafloor by coordinating motions of their five muscular arms. Their arms consist of many repeating segments, requiring them to use a complex control system to coordinate motions among segments and between arms. We conducted in vivo experiments with brittle stars to analyze the functional role of the nerve ring, which connects the nerves in each arm. These experiments were designed to determine how the ophiuroid nervous system performs complex decision-making and locomotory actions under decentralized control. Our results show that brittle star arms must be connected by the nerve ring for coordinated locomotion, but information can travel bidirectionally around the nerve ring so that it circumvents the severance. Evidence presented indicates that ophiuroids rely on adjacent nerve ring connections for sustained periodic movements. The number of arms connected via the nerve ring is correlated positively with the likelihood that the animal will show coordinated locomotion, indicating that integrated nerve ring tissue is critical for control. The results of the experiments should provide a basis for the advancement of complex artificial decentralized systems.
Exploring Innovative Strategies to Enhance Eye-Hand Coordination and Cognitive Functions Through Drone Catching Exercise.
ClinicalTrials.gov study NCT07394231. IPD Sharing: UNDECIDED. Countries: 1. Publications: 10.
Influence of Sensory Stimulation on Sensory Parameters and Motor Function in Children With Developmental Coordination Disorder
ClinicalTrials.gov study NCT06959329. IPD Sharing: UNDECIDED. Countries: 2. Publications: 9.
Functional Movement-power Training for Children With Developmental Coordination Disorder: A Randomised Controlled Trial
ClinicalTrials.gov study NCT02393404. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Functional MRI Study in Children With a Developmental Coordination Disorder (DCD) and/or Developmental Dyslexia (DD)
ClinicalTrials.gov study NCT02393729. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Weak coordination between leaf structure and function among closely related tomato species
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.