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25 results for “local assembly”
Pawpaws prevent predictability: A locally-dominant tree alters understory beta-diversity and community assembly
<p>Data used in "Pawpaws Prevent Predictability: A locally-dominant tree alters understory beta-diversity and community assembly" (Wassel and Myers) accepted for publication in Ecosphere.<br><br><strong>Metadata for Zenodo.pdf </strong>contains more information on the following data files including descriptions of the columns. </p> <p>The file <strong>understory_abundance_data2021.csv</strong> contains all species abundances in 1x1m plots. This data was used for analyses in publication. Each row is a plot, each column is a speceis or plot descriptor, values for columns 5 and higher are species abundances. Data was collected July-August 2021 by Anna Wassel in Missouri, USA. </p> <p>The file <strong>understory_species_list2021.csv </strong>contains a list of the species codes used in the first file with their scientific names and their status as herbs or woody. This was used to filter out herbaceous species from the data set for herbaceous-only analyses. </p> <p> </p>
Text-fig. 1. a: Po Plain and foothills of the Northern Apennine in Northern Italy (inset) with the location of Oriolo (black star) and other Early and Middle Pleistocene plant localities, Enza and Stirone. Red lines indicate the frontal thrust arcs (modified from Martinetto et al. 2015). b: The "La Salita" section, Oriolo and chronology of the two "Sabbie gialle" cycles based on large mammals and palaeomagnetic correlation (modified from Toniato et al. 2017; IMMS 2020* [Italian Mediterranean Marine Stages] updated from Cohen and Gibbars 2020; GTS 2021* [Global Time Scale] updated from Head et al. 2021). c: Quarry "La Salita", Oriolo, in 1987. Main unconformities (U) separating the two "Sabbie gialle" cycles and terrestrial deposits on top are shown. Leaf symbols indicate the positions of some of the layers rich in fossil leaves (photo by G. B. Vai, modified). d: Surroundings of Faenza with the location of Oriolo and adjacent coeval sites yielding plant macrofossils. in The Late Early Pleistocene Flora Of Oriolo, Faenza (Italy): Assembly Of The Modern Forest Biome
Text-fig. 1. a: Po Plain and foothills of the Northern Apennine in Northern Italy (inset) with the location of Oriolo (black star) and other Early and Middle Pleistocene plant localities, Enza and Stirone. Red lines indicate the frontal thrust arcs (modified from Martinetto et al. 2015). b: The "La Salita" section, Oriolo and chronology of the two "Sabbie gialle" cycles based on large mammals and palaeomagnetic correlation (modified from Toniato et al. 2017; IMMS 2020* [Italian Mediterranean Marine Stages] updated from Cohen and Gibbars 2020; GTS 2021* [Global Time Scale] updated from Head et al. 2021). c: Quarry "La Salita", Oriolo, in 1987. Main unconformities (U) separating the two "Sabbie gialle" cycles and terrestrial deposits on top are shown. Leaf symbols indicate the positions of some of the layers rich in fossil leaves (photo by G. B. Vai, modified). d: Surroundings of Faenza with the location of Oriolo and adjacent coeval sites yielding plant macrofossils.
Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia (The genome assembly and annotion fiile)
<p>The genome assembly and annotion fiile used in the manuscript: <strong>Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia</strong></p>
Fig. 5 in Cortical Localization of α- and γ-Tubulin and the Assembly of Cortical Microtubule Cytoskeleton in Hypotrichous Ciliate Euplotes eurystomus
Fig. 5. (A–D) Projections of the optical sections passing through the ventral surface of E. eurystomus cells in mitotic phase decorated with FLUTAX. Scale: 20 μm. (A) The AZM primordium appeared at the bottom-left of old AZM in the early stage of morphogenesis. (AZMP: adoral zone of membranelles primordium; UMP: undulating membrane primordium; arrow shows the UMP originated from the right side of AZMP). (B) The pattern of FVTC primordia was 3-3-3-2-2 from left to right, shown in a box (FVTCP: frontal–ventral–transverse cirri primordium; arrows show the blastema of ALM and PLM originating from the base of FVTCPs). (C) The AZM and UM of proter inherited the olds (white arrow), and those of opisthe were generated from the AZMP (black arrows show the primordium of the left marginal cirri). (D) Some old ciliary organelles still existed until the separation of the proter and opisthe (white arrows show the neonatal ALM and PLM; black arrows show the residual ALM; some old cirri are shown in the circle).
Fig. 3 in Cortical Localization of α- and γ-Tubulin and the Assembly of Cortical Microtubule Cytoskeleton in Hypotrichous Ciliate Euplotes eurystomus
Fig. 3. (A–C) Projection of optical section passing through the ventral surface of E. eurystomus cells decorated with the FLUTAX. Scale: 20 μm. (A) All the ventral ciliary organelles, and especially their base-associated microtubules, were strongly and clearly stained by FLUTAX (ALM: anterior longitudinal microtubules; PLM: posterior longitudinal microtubules; TM: transverse microtubules; PM: peripheral microtubules). (B) The microtubules associated with the adoral ciliary organelles were also marked by FLUTAX (SMB: small membranelle bracket; hollow arrow shows the microtubule fasolculus extending from the base of SMB; white arrow shows the microtubules in the adoral rib; black arrow shows the UM ciliary base–associated microtubules). (C) The FLUTAX decorated the short microtubular bundles between the bases of TCs (arrow).
Fig. 4 in Cortical Localization of α- and γ-Tubulin and the Assembly of Cortical Microtubule Cytoskeleton in Hypotrichous Ciliate Euplotes eurystomus
Fig. 4. (A–D) Projections of the optical sections passing through the dorsal cortex of E. eurystomus cells decorated with FLUTAX. Scale: 20 μm. (A) The leptos microtubular nets covered the dorsal cortex (arrow). (B) The longitudinal microtubules in the dorsal cortex (arrow). (C) The oblique microtubules in the dorsal cortex (arrow). (D) The dargyrome was faintly stained by the FLUTAX.
Fig. 1 in Cortical Localization of α- and γ-Tubulin and the Assembly of Cortical Microtubule Cytoskeleton in Hypotrichous Ciliate Euplotes eurystomus
Fig. 1. The permutation pattern of ciliary organelles in the ventral and dorsal of E. eurystomus cells (A, B). (A) The ventral ciliary pattern of E.eurystomus, (B) the dorsal ciliary pattern of E.eurystomus. (AZM: adoral zone of membranelles, OC: oral cirri; UM: undulating membranes, FVC: frontal–ventral cirri, TC: transverse cirri, CC: caudal cirri, LMC: left marginal cirri DK: dorsal kineties).
Layer-by-Layer siRNA Particle Assemblies for Localized Delivery of siRNA to Epithelial Cells through Surface-Mediated Particle Uptake
<p>Localized delivery of small interfering RNA (siRNA) is a promising approach for spatial control of cell responses at biomaterial interfaces. Layer-by-layer (LbL) assembly of siRNA with cationic polyelectrolytes has been used in film and nanoparticle vectors for transfection. Herein, we combine the ability of particles to efficiently deliver siRNA with the ability of film polyelectrolyte multilayers to act locally. LbL particles were prepared with alternating layers of poly(l-arginine) and siRNA and capped with hyaluronic acid. Negatively charged LbL particles were subsequently assembled on the poly(l-lysine)-functionalized substrate to form a LbL particle-decorated surface. Cells grown in contact with the particle-decorated surface were able to survive, internalize particles, and undergo gene silencing. This work shows that particle-decorated surfaces can be engineered by using electrostatic interactions and used to deliver therapeutic payloads for cell-instructive biointerfaces.</p>
Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"
<p>Trait-based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat-specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habitat-specific species pools produce the locally observed plant assemblages is an ongoing challenge. Here, we evaluated the importance of different processes to community assembly in an alpine fellfield, assessing its effects on local plant trait FD. Using classical randomization tests and linear mixed models, we compared the observed FD with expectations from three null models that hierarchically incorporate additional assembly constraints: stochastic null models (random assembly), independence null models (each species responding individual and independently to abiotic environment), and co-occurrence null models (species responding to environmental variation and to the presence of other species). We sampled species composition in 115 quadrats across 24 locations in the central Pyrenees (Spain) that differed in soil conditions, solar radiation and elevation. Overall, the classical randomization tests were unable to find differences between the observed and expected functional patterns, suggesting that the strong abiotic filters that sort out the flora of extreme regional environments blur any signal of other local processes. However, our approach based on linear mixed models revealed the signature of different ecological processes. In the case of seed mass and leaf thickness, observed FD significantly deviated from the expectations of the stochastic model, suggesting that fine-scale abiotic filtering and facilitation can be behind these patterns. Our study highlights how the hierarchical incorporation of ecological additional constraints may shed light on the dim signal left by local assembly processes in alpine environments.</p>
The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges
<p>Nearly 50 different mouse retinal ganglion cell (RGC) types sample the visual scene for distinct features. RGC feature selectivity arises from its synapses with a specific subset of amacrine (AC) and bipolar cell (BC) types, but how RGC dendrites arborize and collect input from these specific subsets remains poorly understood. Here we examine the hypothesis that RGCs employ molecular recognition systems to meet this challenge. By combining calcium imaging and type-specific histological stains we define a family of circuits that express the recognition molecule Sidekick 1 (Sdk1) which include a novel RGC type (S1-RGC) that responds to local edges. Genetic and physiological studies revealed that Sdk1 loss selectively disrupts S1-RGC visual responses which result from a loss of excitatory and inhibitory inputs and selective dendritic deficits on this neuron. We conclude that Sdk1 shapes dendrite growth and wiring to help S1-RGCs become feature selective.</p>
Files used to develop and test SLAG, Seeded Local Assembly of Genes
<p>This dataset consists of configuration files and results files involved in developing and testing SLAG, an iterative Perl pipeline to construct local assemblies seeded on query sequences. SLAG is intended for situations where a full genome assembly is economically or technically infeasible, and thus it emphasizes methods that can deal with shallow read depth. SLAG and its user-runnable test suite have been deposited at https://github.com/cfcrane/SLAG. This Dryad repository contains files that were used in preparing a manuscript, "SLAG: A Program for Seeded Local Assembly of Genes in Complex Genomes", which has been submitted to Molecular Ecology Resources. The repository is divided into sections for scripts, simulated reads, real reads, and benchmarking against two functionally similar programs, aTRAM2 and SRAssembler.</p>
Files used to develop and test SLAG, Seeded Local Assembly of Genes
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The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges
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Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"
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Maintaining local alkalinity of CO-electroreduction full cell by silica-confined electrocatalysts in membrane electrode assembly
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DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity
<p><span>Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (I) spatial and temporal connectivity of the communities, (II) environmental factors influencing local communities, and (III) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.</span></p>
Data from: Expanding the understanding of local community assembly in adaptive radiations
Communities are thought to be assembled by two types of filters: by the environment relating to the fundamental niche and by biotic interactions relating to the realized niche. Both filters include parameters related to functional traits, and their variation along environmental gradients. Here we infer the general importance of environmental filtering of a functional trait determining local community assembly within insular adaptive radiations on the example of Caribbean Anolis lizards. We constructed maps for the probability of presence of Anolis ecomorphs (ecology-morphology-behavior specialists) on the Greater Antilles and overlaid these to estimate ecomorph community completeness (ECC) over the landscape. We then tested for differences in environmental parameter spaces among islands for real and cross-fitted ECC values to see whether the underlying assembly filters are deterministic (i.e., similar among islands). We then compared information-theoretic models of climatic and landscape parameters among Greater Antillean islands and inferred whether body mass as functional trait determines ECC. We found areas with high ECC to be strongly correlated to environmental filters, partly related to elevation. The environmental parameters influencing high ECC differed among islands. With the exception of the Jamaican twig ecomorph (which we suspect to be misclassified), smaller ecomorphs were more restricted to higher elevations than larger ones which might reflect filtering on the basis of differential physiological restrictions of ecomorphs. Our results in Anolis show that local community assembly within adaptive island radiations of animals can be determined by environmental filtering of functional traits, independently from species composition and realized environmental niche space.
Data from: Expanding the understanding of local community assembly in adaptive radiations
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DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity
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Layer-by-Layer siRNA Particle Assemblies for Localized Delivery of siRNA to Epithelial Cells through Surface-Mediated Particle Uptake
<p>Localized delivery of small interfering RNA (siRNA) is a promising approach for spatial control of cell responses at biomaterial interfaces. Layer-by-layer (LbL) assembly of siRNA with cationic polyelectrolytes has been used in film and nanoparticle vectors for transfection. Herein, we combine the ability of particles to efficiently deliver siRNA with the ability of film polyelectrolyte multilayers to act locally. LbL particles were prepared with alternating layers of poly(l-arginine) and siRNA and capped with hyaluronic acid. Negatively charged LbL particles were subsequently assembled on the poly(l-lysine)-functionalized substrate to form a LbL particle-decorated surface. Cells grown in contact with the particle-decorated surface were able to survive, internalize particles, and undergo gene silencing. This work shows that particle-decorated surfaces can be engineered by using electrostatic interactions and used to deliver therapeutic payloads for cell-instructive biointerfaces.</p>
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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.