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211 results for “functional regionalization”
Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice
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Data from: The Origin Recognition Complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man
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Data from: Forest loss and treeless matrices cause the functional impoverishment of sapling communities in old-growth forest patches across tropical regions
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The internal region of CtIP functions as a regulator of DNA end resection
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Data from: Functional traits in parallel evolutionary radiations and trait-environment associations in the Cape Floristic region of South Africa
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Data from: Disparity in taxonomic and functional diversity of amphibians and reptiles in a tropical region of central Mexico
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Taxonomic, functional and phylogenetic beta diversity of upland forest birds in the Amazon: The relative importance of biogeographic regions, climate, and geographic distance
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Data from: Peptides derived from cadherin juxtamembrane region inhibit platelet function
The juxtamembrane domains (JMD) of transmembrane proteins are rich in critical peptide sequences that participate in dynamic cell signaling events. Synthetic JMD peptides derived from cadherin cell adhesion proteins have previously been shown to modulate platelet function. In this study, we aimed to develop functional bioactive agents from bioinformatically-identified critical peptide sequences. We synthesized overlapping 12-15 amino acids peptides from E- and N-cadherin JMD and assessed their effect on platelet aggregation and platelet ATP secretion. Peptides derived from close to the membrane proximal region inhibit platelet function. Sequential deletion of amino acids from the N- and C-termini of the inhibitory E-cadherin peptides identified the short K756EPLLP763 motif as a critical bioactive sequence. Alanine scanning studies further identified that the dileucine (LL) motif and positively charged lysine (K) are crucial for peptide activity. Moreover, scrambled peptides failed to show any effect on platelet activity. We conclude that peptides derived from JMD of E-cadherin provide potential lead peptides for the development of anti-thrombotic agents and to enable further understanding of the role of cadherins in platelet function.
Data from: Phytoplankton size diversity and ecosystem function relationships across oceanic regions
Trait diversity, a key component of biodiversity, mediates many essential ecosystem functions and services. However, the mechanisms behind such relationships at large spatial scales are not fully understood. Here we adopt the functional biogeography approach to investigate how the size composition of phytoplankton communities relates to primary production and export production along a broad latitudinal gradient. Using in situ phytoplankton size distribution data and a trait-based model, we find an increase in the average phytoplankton size, size diversity, primary production, and export when moving from low to high latitudes. Our analysis indicates that the interplay between spatiotemporal heterogeneities in environmental conditions and a trade-off between the high affinity for nutrients of smaller cells and the ability to avoid predation by larger cells are the main mechanisms driving the observed patterns. Our results also suggest that variations in size diversity alone do not directly lead to changes in primary production and export. The trade-off thus introduces a feedback that influences the relationship between size diversity and ecosystem functions. These findings support the importance of environmentally mediated trade-offs as crucial mechanisms shaping biodiversity and ecosystem function relationships at large spatial scales.
Global analysis of cell behavior and protein localization dynamics reveals region-specific functions for Shroom3 and N-cadherin during neural tube closure
<p>Failures of neural tube closure are common and serious birth defects, yet we have a poor understanding of the interaction of genetics and cell biology during neural tube closure. Additionally, mutations that cause neural tube defects (NTDs) tend to affect anterior or posterior regions of the neural tube but rarely both, indicating a regional specificity to NTD genetics. To better understand the regional specificity of cell behaviors during neural tube closure, we analyzed the dynamic localization of actin and N-cadherin via high-resolution tissue-level time-lapse microscopy during Xenopus neural tube closure. To investigate the regionality of gene function, we generated mosaic mutations in shroom3, a key regulator or neural tube closure This approach elucidates new differences between cell behaviors during cranial/anterior and spinal/posterior neural tube closure, provides mechanistic insight into the function of shroom3 and demonstrates the ability of tissue-level imaging and analysis to generate cell-biological mechanistic insights into neural tube closure.</p>
Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid region
<p>Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation-induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co-occurrence pattern and functionalities along vertical profile (0-500 cm depth) in a semiarid region of China's Loess Plateau. We showed that the effects of afforestation with a deep-rooted legume tree on cropland were greater in deep than that of in top layers, resulting in decreased bacterial beta diversity, more responsive bacterial taxa and functional groups, increased homogeneous selection, and decreased network robustness in deep soils (120-500 cm). Organic carbon and nitrogen decomposition rates and multifunctionality also significantly decreased by afforestation, and microbial carbon limitation significantly increased in deep soils. Moreover, changes in microbial community and functionality in deep layer was largely related to changes in soil moisture. Such negative impacts on deep soils should be fully considered for assessing afforestation's eco-environment effects and for the sustainability of ecosystems because deep soils have important influence on forest ecosystems in semiarid and arid climates. </p>
The ambient noise cross-correlation function and teleseismic events, the Love-wave phase velocities, Rayleigh-wave phase and group velocities and H/V, Vsv and Vsh model in the study region (CNCC)
<p>The cross-correlation functions form EOBSArray (COR_CNCC), The Love-wave phase velocities (Love_phase), Rayleigh-wave phase (Rayleigh_phase) and group velocities (Rayleigh_group) and H/V (HtoV),and 3-D Vsv and Vsh model and related uncertainties (Vsv_Vsh_model) in the study region (CNCC) are archieved in the file named CNCC_data.7z.</p>
FIGURE 1. Pagamea spruceana. A. Flowering branch. B. Fruiting branch. C. Functionally pistillate flower. D in Pagamea spruceana (Rubiaceae, Gaertnereae), a new species from flooded white-sand forests in the Upper Rio Negro region, Brazil
FIGURE 1. Pagamea spruceana. A. Flowering branch. B. Fruiting branch. C. Functionally pistillate flower. D. Ovary with short style in a functionally staminate flower. E. Detail of leaf blade with puberulous margin. A and D from Carvalho 1612, B and E from Prata 1948, C from Prata 1960. Drawn by R. B. de Carvalho.
Essential role of N-terminal SAM regions in STIM1 multimerization and function dataset
<p>The single-pass transmembrane protein Stromal Interaction Molecule 1 (STIM1), located in the endoplasmic reticulum (ER) membrane, possesses two main functions:<br>It senses the ER-Ca2+ concentration and directly binds to the store-operated Ca2+ channel Orai1 for its activation when Ca2+ recedes. At high resting ER-Ca2+ concentration, the ER-luminal STIM1 domain is kept monomeric but undergoes di/multimerization once stores are depleted. Luminal STIM1 multimerization is essential to unleash the STIM C-terminal binding site for Orai1 channels. However, structural basis of the luminal association sites has so far been elusive. Here, we employed molecular dynamics (MD) simulations and identified two essential di/multimerization segments, the α7 and the adjacent region near the α9-helix in the sterile alpha motif (SAM) domain. Based on MD results, we targeted the two STIM1 SAM domains by engineering point mutations. These mutations interfered with higher-order multimerization of ER-luminal fragments in biochemical assays and puncta formation in live-cell experiments upon Ca2+ store depletion. The STIM1 multimerization impeded mutants significantly reduced Ca2+ entry via Orai1, decreasing the Ca2+ oscillation frequency as well as store-operated Ca2+ entry. Combination of the ER- luminal STIM1 multimerization mutations with gain of function mutations and coexpression of Orai1 partially ameliorated functional defects. Our data point to a hydrophobicity-driven binding within the ER-luminal STIM1 multimer that needs to switch between resting monomeric and activated multimeric state. Altogether, these data reveal that interactions between SAM domains of STIM1 monomers are critical for multimerization and activation of the protein.</p>
Data from: Global patterns in helminth host specificity: phylogenetic and functional diversity of regional host species pools matter
Host specificity has a major influence on a parasite's ability to shift between human and animal host species. Yet there is a dearth of quantitative approaches to explore variation in host specificity across biogeographical scales, particularly in response to the varying community compositions of potential hosts. We built a global dataset of intermediate host associations for nine of the world's most widespread helminth parasites (all of which infect humans). Using hierarchical models, we asked if realised parasite host specificity varied in response to regional variation in the phylogenetic and functional diversities of potential host species. Parasites were recorded in 4-10 zoogeographical regions, with some showing considerable geographical variation in observed versus expected host specificity. Parasites generally exhibited the lowest phylogenetic host specificity in regions with the greatest variation in prospective host phylogenetic diversity, namely the Neotropical, Saharo-Arabian and Australian regions. Globally, we uncovered notable variation in parasite host shifting potential. Observed host assemblages for Hydatigera taeniaeformis and Hymenolepis diminuta were less phylogenetically diverse than expected, suggesting limited potential to spillover into unrelated hosts. Host assemblages for Echinococcus granulosus, Mesocestoides lineatus and Trichinella spiralis were less functionally diverse than expected, suggesting limited potential to shift across host ecological niches. By contrast, Hydatigera taeniaeformis infected a higher functional diversity of hosts than expected, indicating strong potential to shift across hosts with different ecological niches. We show that the realised phylogenetic and functional diversities of infected hosts are determined by biogeographical gradients in prospective host species pools. These findings emphasise the need to account for underlying species diversity when assessing parasite host specificity. Our framework to identify variation in realised host specificity is broadly applicable to other host-parasite systems and will provide key insights into parasite invasion potential at regional and global scales.
FIGURE 5 in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIGURE 5 Ancestral area estimation of interspecific MOTUs (A–R) and lineages of Theodoxus obtained from BioGeoBEARS. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. Pie charts represent the relative likelihood of the lineage occurring within Anatolia (dark blue), occurring both within and outside of Anatolia (light blue) and just outside of Anatolia (grey). Small circles with the same colour scheme as the pie charts indicate the most likely state. The bars above the MOTUs represent their current distribution. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Cradle, museum and tap icons represent the relative contributions of functions (cradles, museums and sinks) at different points across the topology for Anatolian diversity. The grey shading indicates the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 1 in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIGURE 1 Operational criteria based on ancestral distributions used to identify and distinguish between the cradle, museum and sink functions. The functions are identifiable by: (a) the cradle function, having an in situ distributed ancestor and descendant with either strict in situ distribution or both in‐ and ex situ distribution, (b) the museum function, having an ancestor with both in‐ and ex situ distribution followed by a descendant with only in situ distribution and (c) the sink function, having an ex situ distributed ancestor with either a strict in situ distribution or with both in‐ and ex situ distribution [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 4 in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIGURE 4 Concentrations of Theodoxus interspecific diversity mapped across the Western Palaearctic using the IDW algorithm. Anatolia shows the highest concentrations of Theodoxus MOTUs. Other regions with more than one Theodoxus MOTUs present are encircled with white‐dashed lines. Bar graphs represent the amount of diversity, indicated by; the number of interspecific MOTUs in each concentrated region, PDand sum ED (see text for details) [Colour figurecanbeviewedat wileyonlinelibrary.com]
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 2 in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIGURE 2 Map of the locations of 376 Theodoxus specimens used in the current study. See Table S1.1 for more information [Colour figure can be viewed at wileyonlinelibrary.com]
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.