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10 results for “odorant responses”
Unexplained Repeated Pregnancy Loss is Associated with Altered Perceptual and Brain Responses to Men’s Body-Odor
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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>
Example Datasets for Iliski - Neuronal calcium, RBC velocities and fUS responses to odorant stimuli in the mouse olfactory bulb
<p>Dataset containing 2 HDF5 files, one per mouse. It is intended to be used to test Iliski, a Transfer Function computation software. Iliski is available on GitLab (<a href="https://gitlab.com/AliK_A/iliski">https://gitlab.com/AliK_A/iliski</a>) along with the User Manual. Refer to the User Manual and to the ReadMe file for more details on Iliski. Data were already published on Zenodo (<a href="https://doi.org/10.5281/zenodo.3773863">https://doi.org/10.5281/zenodo.3773863</a>), but along an old version of the software. This upload is made for clarity purposes.</p> <p>Each file contains acquisitions of responses to odorant stimuli in the olfactory bulb made with :</p> <ul> <li>two-photon linescan microscopy (for Ca2+ and RBC velocity);</li> <li>functional ultrafast ultrasound, acquired from a coronal plane.</li> </ul> <p>HDF5 files tree is as follows :</p> <ul> <li>Data type <ul> <li>Raw : straight out of our extraction software, no specific treatment applied;</li> <li>Aligned : every acquisition has been aligned so that the odor delivery matches the 10 s mark. Acquisitions have also been interpolated to be meaned;</li> <li>Delta : aligned acquisitions are subtracted with the baseline value (between 5 and 10 s);</li> <li>DetaOverBSL : aligned acquisitions are subtracted and then divided with the baseline value.</li> </ul> </li> <li>Data source <ul> <li>Ca : calcium data from GCamP6f expressed in the mitral cells dendritic tufts;</li> <li>RBC : RBC velocities in a capillary near the calcium recording site, simultaneously acquired;</li> <li>FUS : fUS data, coronal plane. Only in FUS folder is two different folders then : High and Lowspeed, corresponding to different filter for fUS treatment, > 80Hz and 10-30Hz respectively.</li> </ul> </li> <li>Stimulation type : Odorant_Quantity_Duration <ul> <li>Odorant type, either Iso Amyl Acetate (AA) or Ethyl tiglate (ET);</li> <li>Odor quantity : measured and calibrated in volt with a photo-ionizator;</li> <li>Odor duration : from 5 s down to 120 ms, a single sniff for a mouse.</li> </ul> </li> </ul> <p>Ca2+ : Calcium</p> <p>fUS : functional ultrafast ultrasound</p> <p>RBC : Red Blood Cell</p>
High-resolution glomerular responses to a large variety of odorants in the mouse olfactory bulb
<p>Imaging of glomerular responses using intrinsic optical signal and synaptopHluorin. </p> <p>Find the software here: <a href="https://doi.org/10.5281/zenodo.3383874">https://doi.org/10.5281/zenodo.3383874</a></p> <p>The paper is here: </p> <p>Soelter, J., Schumacher, J., Spors, H., Schmuker, M.: Computational exploration of molecular receptive fields in the olfactory bulb reveals a glomerulus-centric chemical map. <em>Sci Rep</em> 10, 77 (2020). <a href="https://doi.org/10.1038/s41598-019-56863-4">https://doi.org/10.1038/s41598-019-56863-4</a></p>
Optokinetic response in D. Melanogaster reveals the nature of common repellent odorants
<p>Pre-processed data for the paper "Optokinetic response in D. Melanogaster reveals the nature of common repellent odorants" by Menti et al. (https://doi.org/10.1038/s41598-024-73221-1)</p>
Data from: African elephant dietary responses to odors of monoterpene mixtures and individual monoterpenes
<p>The detoxification limitation hypothesis posits that, unless plant defense compounds interact synergistically or additively to increase their harmful effects, generalist herbivores will prefer consuming combinations of these compounds over singular compounds. Monoterpenes are odoriferous defense compounds that may be toxic to mammalian herbivores when ingested in sufficient quantities. Previous research has shown that the addition of individual monoterpenes to food sources reduces consumption by generalist mammalian herbivores. By using African elephants as a case study, we aimed to determine whether odors from monoterpene combinations (i.e., two or more monoterpenes) also deter generalist mammalian herbivory, and whether generalist herbivores prefer the odors of monoterpene combinations over individual monoterpenes. First, we tested whether the odor of monoterpene combinations that resemble the monoterpene profiles of a high-acceptability, intermediate-acceptability, and low-acceptability plant deter herbivory. We found that elephants preferred plants without the added odors of the monoterpene combinations. Second, we explored how elephants responded to individual monoterpenes found within the combinations compared to the combinations at the same set concentration, and found that the elephants did not always prefer the combinations over the individual monoterpenes. Moreover, the more diverse the combination, the less frequently it was preferred when compared to the individual monoterpene odors. Our results imply that generalist herbivores do not necessarily prefer combinations of plant chemical defenses at comparatively lower concentrations and that, consequently, the composition and diversity of monoterpene profiles in plants likely determine the efficacy of these compounds as an olfactory defense against mammalian herbivory.</p>
Data from: African elephant dietary responses to odors of monoterpene mixtures and individual monoterpenes
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Total RNA-seq of mouse olfactory epithelium in response to single odorants and binary mixtures
GEO Series GSE296359. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
pS6 immunoprecipitation RNA-seq of mouse olfactory epithelium in response to single odorants, binary mixtures, and complex fragrances
GEO Series GSE296360. Mus musculus. 36 samples. Type: Expression profiling by high throughput sequencing.
The Effect of Breast Milk Odor on Pain Response and Salivary Cortisol Level in Preterm Infants
ClinicalTrials.gov study NCT05557435. IPD Sharing: Not stated. Countries: 0. Publications: 0.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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