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4,401 results for “Colon”
Data from: GPCR genes as activators of surface colonization pathways in a model marine diatom
<p>Surface colonization allows diatoms, a dominant group of phytoplankton in oceans, to adapt to harsh marine environments while mediating biofoulings to human-made underwater facilities. The regulatory pathways underlying diatom surface colonization, which involves morphotype switching in some species, remain mostly unknown. Here, we describe the identifications of 61 signaling genes, including G-protein-coupled receptors (GPCRs) and protein kinases, that are differentially regulated during surface colonization in the model diatom species, <em>Phaeodactylum tricornutum</em>. We show that the transformation of <em>P. tricornutum</em> with constructs expressing individual GPCR genes induces cells to adopt the surface colonization morphology. <em>P. tricornutum</em> cells transformed to express GPCR1A display 30% more resistance to UV light exposure than their non-biofouling wild type counterparts, consistent with increased silicification of cell walls associated with the oval-biofouling morphotype. Our results provide a mechanistic definition of morphological shifts during surface colonization and identify candidate target proteins for the screening of eco-friendly, anti-biofouling molecules.</p>
Figure 3 in Phytotelmata colonization in bamboo (Guadua sp.) culms in northeast Argentina
Figure 3. Hypothetic schema of a trophic web for stumps of bamboo community in Corrientes Province, Argentina. The circle represents the schematic stem wall, the arrows indicate energy flow.
Full summary statistics of mixQTL for GTEx v8 Colon_Transverse
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Data and Code: Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi
<p>Raw data and codes underlying the CFU count, qPCR, metabolomics, and NanoSIMS data for the paper "Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi". Data is subdivided by main figure in the paper. Additionally, raw GC-MS datafiles (.cdf) are provided in separate folders. </p>
Raw sequencing data for studying the colonization of soil communities after glacier retreat
<p>Glaciers show a pattern of retreat at the global scale. Deglaciated areas are exposed and colonized by multiple organisms, but lack of global studies hampers a complete understanding of the future of these ecosystems. Until now, the complete reconstruction of soil communities was hampered by the complex identification of organisms, thus analyses at broad geographical and taxonomic scale have been so far impossible. The dataset used for this study represents the assemblages of Bacteria, Mycota, Eukaryota, Collembola (springtails), Oligochaeta (Earth worms), Insecta, Arthropoda and Vascular Plants obtained using environmental DNA (eDNA) metabarcoding. eDNA was extracted from soil samples collected from multiple glacier forelands representative of some of the main mountain chains of Europe, Asia, the Americas and Oceania. We investigated chronosequences of glacier retreat (i.e., the chronological sequence of specific geomorphological features along deglaciated areas for which the date of glacier retreat is known) ranging from recent years to the Little Ice Age (~1850). We used this newly assembled global DNA metabarcoding dataset to obtain a complete reconstruction of community changes in novel ecosystems after glacier retreat. Information on assemblages can be then combined with analyses of soil, landscape and climate to identify the drivers of community changes.</p>
Figure 1 in A new molluscivore crab from Lake Poso confirms multiple colonization of ancient lakes in Sulawesi by freshwater crabs (Decapoda: Brachyura)
Figure 1. Sundathelphusa molluscivora sp. nov. Paratype male (23.5 by 19.0 mm) (ZRC 2000.1703). A, overall view; B, frontal view; C, ventral view.
Figure 3 in A new molluscivore crab from Lake Poso confirms multiple colonization of ancient lakes in Sulawesi by freshwater crabs (Decapoda: Brachyura)
Figure 3. Sundathelphusa molluscivora sp. nov. Paratype male (23.5 by 19.0 mm) (ZRC 2000.1703). A, right side of carapace; B, anterior thoracic sternum; C, left third maxilliped; D, right chelipedal carpus; E, male abdomen; F, right fourth ambulatory leg; G, frontal median triangle. Scale bars: A–F, 5.0 mm; G, 1.0 mm.
Figure 5. Bootstrap 50 in A new molluscivore crab from Lake Poso confirms multiple colonization of ancient lakes in Sulawesi by freshwater crabs (Decapoda: Brachyura)
Figure 5. Bootstrap 50% majority rule consensus tree of phylogenetic relationships within freshwater crabs from Sulawesi, with two species from Thailand used as outgroups, based on maximum parsimony (MP), minimum evolution (ME) and Bayesian inference (BI) (last two with the GTR+I+G model of evolution) topologies. Confidence values from 2000 bootstrap pseudoreplicates (MP/ME) or 2 000 000 generations (BI) based on 562 base pairs of the 16S mitochondrial gene in the order MP/ME/BI; only values above 50% confidence are shown. Abbreviations: Mah, Lake Mahalona; Mat, Lake Matano; Tow, Lake Towuti.
Figure 2 in A new molluscivore crab from Lake Poso confirms multiple colonization of ancient lakes in Sulawesi by freshwater crabs (Decapoda: Brachyura)
Figure 2. Sundathelphusa molluscivora sp. nov. Major chelae. A, male (23.5 by 19.0 mm) (ZRC 2000.1703); B, holotype male (24.6 by 20.4 mm) (MZB 1480); C, female (24.3 by 20.0 mm) (ZRC 2000.1703).
De-colonizing Anthropology - World Anthropological Union Webinar
<p><strong>De-colonizing Anthropology</strong></p><p>WAU - World Anthropological Union Webinar</p><p>Tuesday, November 28, 2pm UTC </p><p> </p><p><strong>Clara Saraiva</strong></p><p>WCAA/ ICS-Universidade de Lisboa</p><p>Convenor</p><p> </p><p><strong>Michel Bouchard</strong></p><p>WCAA/ University of Northern British Columbia </p><p>Web Mediator</p><p> </p><p>Participants:</p><p><strong>Michael B. C. Rivera</strong>/ <strong>趙凱聰</strong>, University of Hong Kong, Hong Kong</p><p><strong>Gcobani Qambela</strong>, University of Johannesburg, South Africa </p><p><strong>Anthony Redmond</strong>, University of Queensland, Australia</p><p><strong>Khaled Furani</strong>, Insaniyyat Association, Palestine</p><p><strong>Hania Sholkamy</strong>, American University Cairo, Egypt</p><p><strong>Gabriela Zamorano</strong>, Centro de Investigaciones y Estudios Superiores en Antropología Social, Mexico</p>
Fig. 3a-j in Physico-chemical characteristics of habitats colonized by the pond snail Radix labiata (Gastropoda, Basommatophora, Lymnaeidae): a model approach
Fig. 3a-j: Graphical presentation of essential parameters associated with logistic regression: white vertical line: position of the maximum probability of occurrence (xmax), black bar: optimum range of the given variable, grey-shaded area: range of the given variable that is still tolerated by the species; a) water temperature, b) pH, c) electric conductivity, d) oxygen content in the water, e) nitrate concentration in the water, f) water depth, g) biological oxygen demand within five days, h) content of ammonium nitrogen, i) geographic altitude, j) current velocity.
Fig. 1 in Physico-chemical characteristics of habitats colonized by the pond snail Radix labiata (Gastropoda, Basommatophora, Lymnaeidae): a model approach
Fig. 1: General habitus of the shell of R. labiata as well as the living animal: a) Front view of the shell (height: 1.4 cm, width: 0.75 cm), b) back view of the shell, c) living animal with its typical triangular tentacles.
Fig. 2a-j in Physico-chemical characteristics of habitats colonized by the pond snail Radix labiata (Gastropoda, Basommatophora, Lymnaeidae): a model approach
Fig. 2a-j: Results of the logistic regression procedure carried out for ten environmental variables: a) water temperature, b) pH, c) electric conductivity, d) oxygen content in the water, e) nitrate concentration in the water, f) water depth, g) biological oxygen demand within five days, h) content of ammonium nitrogen, i) geographic altitude, j) current velocity.
Supplemental Movie 3: Simultaneous dual-color imaging of ICC-SM in the colon and adjacent SMCs.
<p><strong><span>Supplemental Movie 3: Simultaneous dual-color imaging of ICC-SM in the colon and adjacent SMCs.<span> </span></span></strong><span>Video shows spontaneous, propagating Ca<sup>2+</sup> waves through an ICC-SM network along the submucosal surface of the CM in the proximal colon.<span> </span>FOVs are from a muscle of a mouse expressing GCaMP6f in ICC (left FOV; colored green) and RCaMP1.07 in SMCs (right FOV; colored red) imaged simultaneously with a 20x objective. The characteristics of the fluorophores are such that there is minimal spectral overlap. Signals in ICC-SM and SMCs are coordinated, showing initiation of each cycle of Ca<sup>2+</sup> transients in the ICC-SM network followed by activation of SMCs adjacent to ICC-SM. Bottom panel shows traces from fluorescence images:<span> </span>ICC-SM transients (green trace) preceded Ca<sup>2+</sup> signals in SMCs (red trace). Copied with permission from Reference </span><span><span>(133)</span></span><span>.</span></p> <p><strong><span> </span></strong></p>
Support for Baker's law: facultative self-fertilization ability decreases pollen limitation in experimental colonization
<p><strong>Support for Baker’s law: facultative self-fertilization ability decreases pollen limitation in experimental colonization (datasets for paper in the American Journal of Botany)<br></strong></p> <p>There are 2 files associated with this manuscript. The “PLseedsetindividual.csv” file contains seed set for the pollen limitation treatments for each plant in the experimental populations. Pollinator observation data is available in the “pollinator.csv” file</p> <p><br><strong>Description of the data and file structure:</strong></p> <p><strong>PLseedsetindividual.csv</strong></p> <ul> <li>source.population = one of the four source populations used to create our experimental populations</li> <li>autonomy= autonomous selfing category, high or low</li> <li>individual = plant id</li> <li>experimental.population = the id of the experimental population </li> <li>site = site ID</li> <li>size = size of experimental population, single or small</li> <li>date initiated = date experimental population was put in the field</li> <li>dayfromstartofexperiment = derived from date, the time from the start of the experiment that the experimental population was initiated</li> <li>treatment = the pollination treatment for that flower, control or supplemented</li> <li>seed number = seed set for the treated flower</li> </ul> <p><br><strong>Pollinator.csv</strong></p> <ul> <li>experimental.population = the id of the experimental population </li> <li>site = site ID</li> <li>start.date = day experimental population was initiated</li> <li>end.date = day the experimental popuation was taken out of the field</li> <li>source population = one of the four source populations used to create our experimental populations</li> <li>autonomy= autonomous selfing category, high or low</li> <li>size = size of experimental population, single or small</li> <li>number of plants = number of plants in the experimental population </li> <li>flowers day x (1–4) = number of flowers on day 1</li> <li>males day x (1-4) = number of flowers on day X</li> <li>day.<em>x</em>.poll.date = date of day 1 or day 2 pollinator observation </li> <li>day.<em>x</em>.poll.time = time of day 1 or day 2 pollinator observation </li> <li>bb.day.<em>x</em>, mb.day.x,, sb.day.x., = bumblebee, medium bee, small bee visits on day 1 or day 2</li> <li>total.poll.visits = The total number of pollinator visits across day 1 and day 2</li> <li>visits.per.flower = the number of flowers was averaged across day 1 and day 2. The total number of visits were then divided by the average flower number.</li> </ul>
Data and code for: Pneumococcus co-colonization and the stress-gradient-hypothesis
<p>Pneumococcus serotype co-colonization, caused by the polymorphic bacteria <em>Streptococcus pneumoniae</em>, has been increasingly investigated and reported in recent years. Yet, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of these bacteria. Here we report on a rich dataset of cross-sectional pneumococcal colonization studies collected from the literature, where we quantified patterns of transmission intensity and co-colonization variation in children populations across different epidemiological settings. Fitting these data to an SIS model with co-colonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity R<sub>0</sub> and susceptibility to co-colonization <em>k</em>, in support of the stress-gradient-hypothesis (SGH) in ecology. According to this hypothesis, ecological interactions between organisms shift positively as environmental stress increases. In our model higher environmental stress is represented via lower values of the basic reproduction number R<sub>0</sub>, and a shift towards positive interactions is represented via higher vulnerability to co-colonization (higher <em>k</em>) between pneumococcus serotypes.</p>
FIGURE 4 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 4. Ordovician bryozoan colony. One-half of hemispherical bryozoan, interior of object, bearing probably oldest boring attributable to ichnogenus Entobia Bronn, 1837. Besides semi-radial tunnels and exploratory threads, three bulbous chambers discovered near the center of the hemisphere. Darriwilian (middle Ordovician), Khrevitsa locality, St. Petersburg Region, Russia. Scale bar equals 1 cm.
FIGURE 7 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 7. Three-dimensional visualization of a shell of the recent Foraminifera Amphistegina sp. illustrating the potential of micro-CT in investigations of recent marine shelled organisms. (A) A surface view of the whole shell. (B) A transversal section through the whole shell (C, D) Details of the shells´s surface.
FIGURE 5 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 5. Minute conulariid specimen. (A) Conulariid specimen of Archaeoconularia fecunda and trepostome bryozoan colony; coated with ammonium chloride, no. NMP L21990, locality Loděnice, Upper Ordovician, Zahořany Formation (lower Katian) (B) Micro-CT visualizing of inner surfaces. Scale bar equals 5 mm.
FIGURE 3 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 3. Siliceous nodules of the Šárka Formation. (A, B) Pricyclopyge binodosa, complete trilobite, no. NMP L 35055, locality Praha-Šárka, Middle Ordovician (Darriwilian), (A) Enrolled trilobite coated with ammonium chloride, exterior of objects. (B) Micro-CT image showing dense burrows, interior of objects. (C, D) Rostrum with eyes of a trilobite P. binodosa, no. NMP L46892, locality Praha-Šárka, Middle Ordovician (Darriwilian). (C) Rostrum coated with ammonium chloride, exterior of objects. (D) Micro-CT visualization of tunnels, interior of objects. (E) Bivalve Redonia deshayesi, micro-CT image showing trace fossils, interior of objects, no. NMP L 51722, locality Osek, Middle Ordovician (Darriwilian). All scale bars equal 5 mm.
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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.