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455 results for “mushroom”
Mushrooms
<p>This data set includes descriptions of hypothetical samples corresponding to 23 species of gilled mushrooms in the Agaricus and Lepiota Family</p>
Supplementary material for Targeted gene knock-in reduces variation between transformants in the mushroom-forming fungus Schizophyllum commune
<p>Supplementary data for "Targeted gene knock-in reduces variation between transformants in the mushroom-forming fungus <em>Schizophyllum commune</em>"</p> <p>Dataset consists of fluorescent images of <em>S. commune</em> strains with an ectopic or targeted integration of <em>dTomato </em>under the control of the <em>tubulin </em>promoter and <em>hom2 </em>terminator and the obtained fluorescent intensity of each strain. For thesholding the mean intensity of all pixels above 14 (range 0, 255) was calculated.</p> <p>Files are names according to strain (E1-E12 for ectopic integrations and TI1-TI6 for targeted integrations and WT for wildtype) and replicate.</p>
Calcium imaging of odor responses in the fruit fly mushroom body
<p><strong>Abstract</strong></p> <p>This dataset contains olfactory responses in the third stage of the olfactory circuit in fruit flies: the mushroom body. The responses are recorded with the GCaMP3 sensor. The methods used to collect the data and the procedures to process them are presented in detail in Campbell et al., 2013, Journal of Neuroscience. The dataset was also used in a recent manuscript by Srinivasan et al., 2023.</p> <p><strong>Methods</strong></p> <p>Please refer to Campbell et al., 2013, Journal of Neuroscience for details. Here, we present a description of how the data was collected, the odors presented, and the analysis, excerpted from Campbell et al., 2013.</p> <p><strong>Animal preparation</strong></p> <p>Flies carrying the genetically encoded calcium sensor UAS-GCaMP3 (Tian et al., 2009) were crossed with OK107-Gal4 flies (Connolly et al., 1996) to drive GCaMP3 expression in essentially all KCs (Lee and Luo, 1999; Aso et al., 2009). All experiments were conducted on female F1 heterozygotes from this cross, aged 2–5 d post-eclosion. Procedures for animal preparation were as described previously (Turner et al., 2008; Murthy and Turner, 2010; Honegger et al., 2011). Flies were anesthetized temporarily on ice and inserted into a small hole cut in the recording platform. The animal’s head was tilted forward, exposing the olfactory organs to the odor delivery nozzle located on the underside of the plat- form. The fly was fixed in place with fast-drying epoxy (Devcon 5 min epoxy). The top of the fly was bathed in oxygenated saline (Wilson et al., 2004) and the cuticle overlying the brain was dissected away. Air sacs overlying the MBs were pushed aside, but we did not attempt to remove the perineural sheath. To minimize movement of the brain inside the head capsule, we removed the pulsatile organ at the neck and the probos- cis retractor muscles that pass over the caudal aspect of the optic lobes.</p> <p> </p> <p><strong>Odor delivery </strong></p> <p>The following chemicals were used as stimuli: 2-heptanone (CAS #110-43- 0), 3-octanol (CAS #589-98-0), 6-methyl-5-hepten-2-one (CAS #110-93-0), ␣-humulene (CAS #6753-98-6), benzaldehyde (CAS #100-52-7), ethyl lactate (CAS #97-64-3), ethyl octanoate (CAS #106-32-1), hexanal (CAS #66-25-1), isoamyl acetate (CAS #123-92-2), 4-methylcyclo- hexanol (CAS #589-91-3), methyl octanoate (CAS #111-11-5), diethyl suc- cinate (CAS #123-25-1), pentanal (CAS #110-62-3), butyl acetate (CAS #123-86-4), 1-octen-3-ol (CAS #3391-86-4), 1-hepten-3-ol (CAS #4938-52- 7), and pentyl acetate (CAS #628-63-7). Odors were presented using a custom-built delivery system that uses serial air dilutions to control odor concentration while maintaining a constant total airflow of 1 L/min at the fly. Experiments were conducted at an odor dilution of 1:100 or, where appropriate, adjusted to match the concentrations used behaviorally. We used a photo-ionization detector (Aurora Scientific) to match concentrations between the imaging rig and the T-maze and to monitor odor delivery throughout each imaging ex- periment. Odor pulses were created by switching between clean and odorized air streams using a synchronous two-way valve (N-Research). This final valve was located 50 cm from the fly, leading to a delay of 300 ms between valve switching and the odor reaching the fly. The flow path was 1/8 inch in diameter throughout, which enabled the system to work near atmospheric pressure at these flow rates. The distance of the valve from the fly and the large tubing diameter virtually eliminated pressure transients caused by valve switching, as measured by the photo-ionization detector and a hot-wire anemometer.</p> <p><strong>Calcium imaging</strong></p> <p>Two-photon imaging was performed using a Prairie Ultima system (Prairie Technologies) and a Ti-Sapphire laser (Chameleon XR; Coher- ent) tuned to 920 nm delivering 8 –10 mW at the sample. All images were acquired with Olympus water-immersion objectives (LUMPlanFl/IR, 60x, numerical aperture 0.9; LUMPlanFl/IR, 40x, numerical aperture 0.8). Imaging planes were selected to maximize the number of visibleKCs. Typically imaging frames were 300 x 300 pixels, acquired with a pixel dwell time of 1.6 s, yielding frame rates near 3.8 Hz. On average, 120 KCs (range: 60 –170) were monitored in one plane. Custom MATLAB (MathWorks) routines were used to control odor presentation and synchronize stimulus delivery with data acquisition. Data were acquired in 20 s sweeps with a 1 s odor pulse triggered 8 s after sweep onset. The interstimulus interval was 25 s. Stimuli were presented in randomly interleaved fashion, adjusted so that the same odor was never presented twice in succession.</p> <p><strong>Imaging analysis</strong></p> <p>Data were analyzed using MATLAB and R (http://www.R-project.org). To correct for motion within the field of view, frames were aligned using 2D image registration approaches. In many cases, a Fourier-based sub-pixel translation correction was sufficient (Guizar-Sicairos et al., 2008). Some animals required an affine transform to cope with global distortions, such as rotational movement of the brain (Thirion, 1998). Where necessary a nonrigid transform was used to correct more localized dis- tortions (Klein et al., 2010). Fluorescent neural tissue was automatically segmented from the surrounding regions. Pixel intensity values from the area outside this boundary were considered to represent background (tissue autofluorescence plus shot noise) and the mean pixel intensity value from the back- ground was then subtracted from the overall image. To quantify the response of the KCs a small, circular region of interest 6 – 8 pixels in diameter was applied to each cell body. This allowed aver- aging of the pixel intensity values from each cell, treating individual KCs as separate units. Care was taken to ensure that each selected cell re- mained within its region of interest over the whole imaging session. Response amplitudes were calculated as the mean change in fluorescence (dF/F) in the 0.5– 4.5 s window after stimulus onset. A statistical test originally described in Honegger et al. (2011) was used to determine whether a KC responded significantly on a given trial. Briefly, the SD of the baseline activity was obtained 8 s before stimulus onset. The response time course was then smoothed using a five-point running average to control for outliers. The peak dF/F in the 0.5– 4.5 s window after stimulus onset was determined. The response was judged to be significant if this peak was 2.33 SDs greater than the baseline, which corresponds to a one-tailed significance test where alpha = 0.01.</p> <p><br> <strong>References</strong></p> <p>Aso Y, Grübel K, Busch S, Friedrich AB, Siwanowicz I, Tanimoto H (2009) The mushroom body of adult Drosophila characterized by GAL4 drivers. J Neurogenet 23:156 –172. </p> <p>Connolly JB, Roberts IJ, Armstrong JD, Kaiser K, Forte M, Tully T, O’Kane CJ (1996) Associative learning disrupted by impaired Gs signaling in Drosophila mushroom bodies. Science 274:2104 –2107.</p> <p>Honegger KS, Campbell RA, Turner GC (2011) Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body. J Neurosci 31:11772–11785.</p> <p>Lee T, Luo L (1999) Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22:451– 461.</p> <p>Murthy M, Turner GC (2010) In vivo whole-cell recordings in the Drosophila brain. In: Drosophila neurobiology methods: a laboratory manual (Zhang B, Waddell S, Freeman M, eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.</p> <p>Srinivasan, S., Daste, S., Modi, M., Turner, G., Fleischmann, A. & Navlakha, S (2023). Stochastic coding: a conserved feature of odor representations and its implications for odor discrimination. bioRxiv.</p> <p>Thirion JP (1998) Image matching as a diffusion process: an analogy with Maxwell’s demons. Med Image Anal 2:243–260.</p> <p>Tian L, Hires SA, Mao T, Huber D, Chiappe ME, Chalasani SH, Petreanu L, Akerboom J, McKinney SA, Schreiter ER, Bargmann CI, Jayaraman V, Svoboda K, Looger LL (2009) Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods 6:875–881.</p> <p>Turner GC, Bazhenov M, Laurent G (2008) Olfactory representations by Drosophila mushroom body neurons. J Neurophysiol 99:734 –746.</p> <p>Wilson RI, Turner GC, Laurent G (2004) Transformation of olfactory representations in the Drosophila antennal lobe. Science 303:366–370.</p> <p><strong>Usage notes</strong></p> <p>The files are all in csv format, and can be easily opened in R or Python or other programming languages.</p> <p>Please see the README.md file for directions on how to use the data.</p> <p>The dataset included here is broken into two parts. The main dataset was the one that was chiefly used in the Campbell and Srinivasan papers, with the second part containing 7 additional datasets that were used in some figures. A fuller description is available in the README.md file.</p>
mushrooms
<p>Dataset con diferentes caracteristicas de hongos</p>
Fig. 3 in Anthomastus nanhaiensis, new species, and Bathyalcyon robustum Versluys, 1906, two mushroom soft corals (Octocorallia: Coralliidae) from Zhenbei Seamount in the South China Sea
Fig. 3. Sclerites of Anthomastus nanhaiensis, new species. A, sclerites from autozooid tentacle tip; B, sclerites from tentacle base; C, sclerites from pharynx. Scale bars = 0.10 mm (A, B), and 0.05 mm (C).
Fig. 2 in Anthomastus nanhaiensis, new species, and Bathyalcyon robustum Versluys, 1906, two mushroom soft corals (Octocorallia: Coralliidae) from Zhenbei Seamount in the South China Sea
Fig. 2. Morphology of the holotype of Anthomastus nanhaiensis, new species. A, the animal in situ; B, an autozooid; C, the colony in top view; D, the colony in lateral view; E, the longitudinal section of the colony, showing large cavities of autozooids (au) and small cavities of siphonozooids (arrows). Scale bars = 1 mm (B), 10 mm (C‒E).
Fig. 7 in Anthomastus nanhaiensis, new species, and Bathyalcyon robustum Versluys, 1906, two mushroom soft corals (Octocorallia: Coralliidae) from Zhenbei Seamount in the South China Sea
Fig. 7. Sclerites of Bathyalcyon robustum Versluys, 1906. A, sclerites from tentacle pinnules of autozooids; B, sclerites from tentacle rachis of autozooids; C, sclerites from anthocodial wall. Scale bars = 0.10 mm.
Fig. 8 in Anthomastus nanhaiensis, new species, and Bathyalcyon robustum Versluys, 1906, two mushroom soft corals (Octocorallia: Coralliidae) from Zhenbei Seamount in the South China Sea
Fig. 8. Sclerites of Bathyalcyon robustum Versluys, 1906. A, sclerites from pharynx; B, sclerites from outermost anthostelar coenenchyme; C, sclerites from deeper layer of coenenchyme; D, sclerites from holdfast. Scale bars = 0.10 mm.
Fig. 5 in Anthomastus nanhaiensis, new species, and Bathyalcyon robustum Versluys, 1906, two mushroom soft corals (Octocorallia: Coralliidae) from Zhenbei Seamount in the South China Sea
Fig. 5. Sclerites of Anthomastus nanhaiensis, new species. A, sclerites from surface of stalk; B, sclerites from interior of stalk. Scale bars = 0.10 mm.
Fig. 4 in Anthomastus nanhaiensis, new species, and Bathyalcyon robustum Versluys, 1906, two mushroom soft corals (Octocorallia: Coralliidae) from Zhenbei Seamount in the South China Sea
Fig. 4. Sclerites of Anthomastus nanhaiensis, new species. A, sclerites from surface of capitulum; B, sclerites from interior of capitulum. Scale bars = 0.10 mm.
Fig. 6 in Anthomastus nanhaiensis, new species, and Bathyalcyon robustum Versluys, 1906, two mushroom soft corals (Octocorallia: Coralliidae) from Zhenbei Seamount in the South China Sea
Fig. 6. Morphology of Bathyalcyon robustum Versluys, 1906. A, MBM286427 in situ; B, clonies in aggregation with MBM286428 in the most right; C, MBM286427 in preservation; D, MBM286428 in preservation; E, siphonozooids; F, transverse section through middle anthostele of MBM286427, showing pharynx and mesenteries. Scale bars = 10 mm (C, D), 0.5 mm (E), and 5 mm (F).
FIGURE 16 Periclimenes incertus Borradaile, 1915 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 16 Periclimenes incertus Borradaile, 1915, ovigerous female, RMNH.CRUS.D.53946. A, left major second pereiopod; B, idem, chela; C, right minor second pereiopod; D, idem Downloaded, chelafrom. Scale Brill. bar com: A,12 C/= 121/mm 2023; 03:02:30PM B, D = 0.2 mm. via Open Access. This is an open access article distributed under the terms of the prevailing CC-BY license at the time of publication. https://creativecommons.org/licenses/by/4.0/
FIGURE 14 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 14 Periclimenes subcorallum sp. nov., ovigerous female paratype (pocl. 1.45 mm), RMNH.CRUS.D.57575. A, telson; B, idem, detail distal part; C, distolateral part of uropod exopod; D, right first pleiopod. Male paratype (pocl. 1.35 mm), RMNH.CRUS.D.57575. E, right first pleiopod; F, right second pleopod. Scale bar: A, C, E = 0.4 mm; B = 0.07 mm; D, F = 0.2 mm.
FIGURE 15 Periclimenes incertus Borradaile, 1915 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 15 Periclimenes incertus Borradaile, 1915, ovigerous female, RMNH.CRUS.D.53946. A, rostrum and anterior appendages, dorsal view; B, idem, lateral view; C, left first pereiopod; D, idem, chela; E, idem, proximal segments; F, fourth thoracic sternites and proximal segments of first pereiopods. Scale bar: A–C = 1 mm; D–E = 0.2 mm; F = 0.4 mm.
FIGURE 5 Periclimenes watamuae Bruce, 1976a, minor second pereiopod. A. male, 1.00 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 5 Periclimenes watamuae Bruce, 1976a, minor second pereiopod. A. male, 1.00 mm, left P2, RMNH.CRUS.D.57574, LEM.36; B, ovigerous female, pocl 1.45 mm, right P2, RMNH.CRUS.D.57574, LEM.36; C, ovigerous female, pocl. 1.40 mm, right P2, RMNH.CRUS.D.57574, GenBank MK843275. Scale bar = 0.4 mm.
FIGURE 12 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 12 Periclimenes subcorallum sp. nov., ovigerous female paratype (pocl. 1.45 mm), RMNH.CRUS.D.57575. A, left major second pereiopod; B, idem fingers of chela; C, idem, tip of fingers, setae omitted; D, right minor second pereiopod; E, idem, fingers of chela. Scale bar: A, D = 1 mm; B, E = 0.2 mm; C = 0.07 mm.
FIGURE 11 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 11 Periclimenes subcorallum sp. nov., ovigerous female paratype (pocl. 1.45 mm), RMNH.CRUS.D.57575. A, left second maxiliped; B, left third maxilliped; C, left first pereiopod; D, idem, proximal segments; E, idem, chela. Scale bar: A, D, E = 0.2 mm; B = 0.4 mm; C = 1 mm.
FIGURE 6 Periclimenes diversipes Kemp, 1922, ovigerous female. A, stn LEM.07 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 6 Periclimenes diversipes Kemp, 1922, ovigerous female. A, stn LEM.07, on Danafungia scruposa; B, stn Downloaded from Brill.com 12/12/2023 03:02:30PM LEM.07, on Lithophyllon via repanda; Open C, stn AccessLEM..18 This, onis an Sandalolitha open accessrobustaarticle. distributed under the terms of the prevailing CC-BY license at the time of publication. https://creativecommons.org/licenses/by/4.0/
FIGURE 4 Periclimenes watamuae Bruce, 1976a, major second pereiopod. A in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 4 Periclimenes watamuae Bruce, 1976a, major second pereiopod. A, male, pocl 1.00 mm, right P2, RMNH. CRUS.D.57574, LEM.36; B, ovigerous female, pocl 1.45 mm, left P2, RMNH.CRUS.D.57574, LEM.36; C, ovigerous female, pocl. 1.40 mm, left P2, RMNH.CRUS.D.57574, GenBank MK843275. Scale bar = 0.4 mm.
FIGURE 3 Periclimenes diversipes Kemp, 1922, minor second pereiopod. A in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 3 Periclimenes diversipes Kemp, 1922, minor second pereiopod. A, male, pocl 1.38 mm, left P2, RMNH.CRUS.D.57553, GenBank MK843283; B, ovigerous female pocl. 1.25 mm, left P2, RMNH. CRUS.D.57547, GenBank MK843284; C, idem, lateral aspect chela; D, female pocl. 1.25 mm, right P2, RMNH.CRUS.D.57548, GenBank MK843295; E, ovigerous female pocl. 1.63 mm, right P2, RMNH. CRUS.D.57551, GenBank MK843282. Scale bar = 0.4 mm.
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)
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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.