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93 results for “zonation”
Dataset and R code used in "Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes"
<p>Dataset and R code used for the manuscript:</p> <p>Von Eggers, J. M., Wisnoski, N. I., Calder, J. W., Capo, E., Groff, D. V., Krist, A. C., & Shuman, B. (2024). Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. <em>Environmental Microbiology</em>, 26(3), e16607.</p> <p>This dataset and code are also available on GitHub (<a href="https://github.com/jvoneggers/WYLakeSedMicrobes">https://github.com/jvoneggers/WYLakeSedMicrobes</a>).</p>
SPT results - Simulation of zonation-function relationships in the liver using coupled multiscale models: Application to drug-induced liver injury
<p>Results of the study "Simulation of zonation-function relationships in the liver using coupled multiscale models: Application to drug-induced liver injury"</p>
Data from: Single cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice
<p>2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (<em>Rspo3</em>) and pericentral <em>Apc</em>, suggested dysregulation of the Wnt/β-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies.</p>
Fig. 4 in Vertical Zonation And Heat Tolerance Of Three Littorinid Gastropods On A Rocky Shore At Tanjung Chek Jawa, Singapore
Fig. 4. Mean glutamate oxaloacetate transaminase (GOT) activities (µmol NADH/min/g wet weight) of Littoraria sp., Echinolittorina malaccana and E. vidua from Tanjung Chek Jawa at four temperatures: 25 °C, 45 °C, 50 °C and 55 °C. (Vertical bars represent standard errors). Littoraria sp. ●––––●; Echinolittorina malaccana, ●........●; E. vidua ■-------■.
Fig. 2 in Vertical Zonation And Heat Tolerance Of Three Littorinid Gastropods On A Rocky Shore At Tanjung Chek Jawa, Singapore
Fig. 2. Kite diagrams showing the distributions of Littoraria spp. (LL), Echinolittorina malaccana (EM) and E. vidua (EV) on a sloping rock (angle of elevation of approximately 35.6°) at Tanjung Chek Jawa. (MHWS is represented by dashed line).
Fig. 1 in Vertical Zonation And Heat Tolerance Of Three Littorinid Gastropods On A Rocky Shore At Tanjung Chek Jawa, Singapore
Fig. 1. Kite diagrams showing the distributions of Littoraria spp. (LL) and Echinolittorina malaccana (EM) on a vertical rock at Tanjung Chek Jawa in (a) June/July, (b) September, and (c) December 2002. (MHWS is represented by dashed line).
Fig. 3 in Vertical Zonation And Heat Tolerance Of Three Littorinid Gastropods On A Rocky Shore At Tanjung Chek Jawa, Singapore
Fig. 3. Probit response curves of Littoraria sp. (●), Echinolittorina vidua (●) and E. malaccana (■), from which the 1h LT50 values are obtained.
Text-fig. 4. Lithostratigraphy of the BCB and standard ammonite zonation in relation to Schloenbachia lymensis occurrence. a. Plaňany. b. Slaný. Dashed lines indicate chronostratigraphic ranges of marine strata in both localities. For detailed litho- and biostratigraphy of the Pecínov Member see Košťák et al. (2018). in Taxonomy And Stratigraphic Distribution Of The Ammonite Schloenbachia Neumayr, 1875 From The Bohemian Cretaceous Basin
Text-fig. 4. Lithostratigraphy of the BCB and standard ammonite zonation in relation to Schloenbachia lymensis occurrence. a. Plaňany. b. Slaný. Dashed lines indicate chronostratigraphic ranges of marine strata in both localities. For detailed litho- and biostratigraphy of the Pecínov Member see Košťák et al. (2018).
Data from: Single cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice
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DNA metabarcoding data: Altitudinal zonation of green algae biodiversity in the French Alps
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Zonation of mangrove flora and fauna in a subtropical estuarine wetland based on surface elevation
<p>In the context of sea-level rise (SLR), an understanding of the spatial distributions of mangrove flora and fauna is required for effective ecosystem management and conservation. These distributions are greatly affected by tidal inundation, and surface elevation is a reliable quantitative indicator of the effects of tidal inundation. Most recent studies have focused exclusively on the quantitative relationships between mangrove-plant zonation and surface elevation, neglecting mangrove fauna. Here, we measured surface elevation along six transects through the mangrove forests of a subtropical estuarine wetland in Zhenzhu Bay (Guangxi, China), using a real-time kinematic global positioning system. We identified the mangrove plants along each transect and investigated the spatial distributions of arboreal, epifaunal, and infaunal molluscs, as well as infaunal crabs, using traditional quadrats. Our results indicated that 97.3% of all mangrove forests in the bay were distributed within the 400–750 m intertidal zone, between the local mean sea level and mean high water (119 cm above mean sea level). Mangrove plants exhibited obvious zonation patterns, and different species tended to inhabit different niches along the elevation gradient: <i>Aegiceras corniculatum</i> dominated in seaward locations while <i>Lumnitzera racemosa</i> dominated in landward areas. Mangrove molluscs also showed distinct patterns of spatial zonation correlated with surface elevation, independent of life-form and season; the spatial distributions of some molluscs were influenced by the relative abundances of certain mangrove plants. In contrast, the spatial distributions of crabs in the bay were not correlated with surface elevation. To the best of our knowledge, this is the first study to explicitly quantify the influences of surface elevation on the spatial distributions of mangrove fauna in the intertidal zone. This characterization of the vertical ranges of various flora and fauna in mangrove forests provides a basic framework for future studies aimed at predicting changes in the structure and functions of mangrove forests in response to SLR.</p>
Rhizophora zonation, salinity, and nutrients in the western Atlantic
Rhizophora is the dominant genus of mangrove forests on the Atlantic coast of northern South America. What determines the zonation frequently observed in sympatric populations of the two neotropical species R. mangle, R. racemosa, and their hybrids, R. × harrisonii, is an open question. The most widely held hypothesis is that differences in salinity tolerance among the taxonomic groups explains the observed zonation. To address this question, we analyzed the elemental composition of soils and canopy leaves from 60 Rhizophora spp. trees distributed in different intertidal zones of an estuarine site of the Paria Gulf, Venezuela. The low intertidal zone showed lower salinity, organic matter, C, N, S, and Na, and higher bulk density, Al, Fe, and Mn concentrations compared with the higher intertidal zones. Using morphological characters and microsatellite molecular markers, we identified 39 pure R. mangle, 19 hybrids, and only two pure R. racemosa. We found that both intertidal position and taxonomic groups explained most of the differences in leaf variables measured across trees. The ratio Mg/Ca, however, was higher in R. mangle than in R. racemosa and hybrids regardless of intertidal position. Moreover, at some specific intertidal position, R. mangle differed from R. racemosa and hybrids in the values of C, N, K, Mg, Fe, Mn, C/N, K/Ca, S/Ca, and d13C. We conclude that despite the scarcity of R. racemosa and the absence of a clear species zonation, our results suggest that R. mangle copes with salinity differently than R. racemosa and R. × harrisonii.
Supplementary Files - Transcriptomic analysis of CPM-positive hiPSCs-derived liver progenitor cells in a microfluidic device shows zonation-like patterns.
<p>Supplementary Files for the paper intitled Transcriptomic analysis of CPM-positive hiPSCs-derived liver progenitor cells in a microfluidic device shows zonation-like patterns. </p>
Data from U and Th zonation in apatite observed by synchrotron X–ray fluorescence tomography and implications for the (U–Th)/He system Sousa et al 2024
<p>Data from </p> <p><span>U and Th zonation in apatite observed by synchrotron X–ray fluorescence tomography and implications for the (U–Th)/He system</span></p> <p><span>Sousa et al</span></p> <p><span>Geochronology</span></p>
Data repository - Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis
<p>Data associated with the manuscript entitled "Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis".</p> <p>Files:</p> <p>table_A_LCM_TPM_values.tsv: Gene expression levels of microdissected villus quintiles. First column is the ensemble gene id. Next 15 columns are the raw Kallisto TPM values for villus segments 1 (bottom) to 5 (top) for three different mice (a to c). Additional columns include the external gene name, description, and gene biotype.</p> <p>table_B_scRNAseq_UMI_counts.tsv: Raw UMI counts of cells that were utilized in this study. Analysis is based on raw data from the NCBI GEO datasets GSM2644349 and GSM2644350. Each of the columns represents a single cell, column headers are the corresponding cell barcodes and enable retrieval of tSNE coordinates from table_C_scRNAseq_tsne_coordinates_zones.tsv. Values represent raw UMI counts.</p> <p>table_C_scRNAseq_tsne_coordinates_zones.tsv: tSNE coordinates and reconstructed zones of cells that were utilized in this study. Tab separated text file. Analysis is based on raw data from the NCBI GEO datasets GSM2644349 and GSM2644350. Columns: cell_id: cell barcode, corresponds to column header of Table S2. Seurat tSNE coordinate 1 and tSNE coordinate 2. Last column is the inferred zone (Crypt, V1..V6).</p> <p>table_D_zonation_reconstruction.tsv: Zonation table of reconstructed scRNAseq data. Tab separated text file. Columns: Gene names: gene id, mean expression in each of the crypt zone and 6 villus zones, standard error of the means in the Crypt zone and 6 villus zones, p-value and q-value for the zonation profiles.</p> <p>raw_data.zip: The raw and intermediary data for runnning the scripts in <a href="https://github.com/aemoor/Code_spatial_reconstruction_enterocytes">https://github.com/aemoor/Code_spatial_reconstruction_enterocytes</a></p>
Effects of salt marsh vegetation zonation on carbon and nitrogen cycling in Connecticut
<p>Coastal marshes fringing the Long Island Sound (Connecticut, USA) are dynamic ecosystems positioned at the interface between land and sea, and provide an array of essential ecosystem services to society associated with improved water quality, carbon sequestration, and disturbance regulation. However, these wetlands are increasingly altered by rising seas and invasive species, and have been affected by historical management such as tidal manipulation. We conducted a survey of 20 Connecticut salt marshes (10 tidally restored, 10 unrestricted references) in 2017 to quantify carbon mineralization, denitrification potential, microbial community composition, a<span>bove and belowground biomass and a suite of sediment characteristics. Carbon density was our only paramenter that differed between unrestricted and tidally restored marshes, but we observed strong differences across vegetation zones, with vegetation being a top predictor of microbial respiration and potential denitrification rates. Based on sea-level rise model projections, the replacement of <i>S. patens</i> by short-form <i>S. alterniflora</i> is expected to be widespread across the Connecticut coastline, decreasing statewide potential denitrification from the low-to-high marsh transitional zone. Our results suggest that changes in vegetation zones can serve as landscape-scale predictors of the rapid changes occurring in salt marshes.</span></p>
Prioritization – ZONATION of Šumava National Park
<p>The final raster layer of prioritization created by using ZONATION software. It is a result of our analyses: we made habitat suitability models for fifty species and used a habitat mapping layer – a detailed description of natural habitats with its older and updated version of the layer.</p> <p>These biodiversity features were inputs for ZONATION. The algorithm starts from the whole landscape and iteratively removes pixels of the raster of the lowest conservation value. We used ABF (additive benefit functions) algorithm, which emphasizes locations with many occurrences of different species and richness of the inputs.</p> <p>The final file divides Šumava NP (our study area) into one hundred same pieces according to its conservation priority.</p>
Data from: Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada
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Prioritization – ZONATION of Šumava National Park
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Data from: Zonation of mangrove flora and fauna in a subtropical estuarine wetland based on surface elevation
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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.