OSCR

The olfactory receptor SNIF-1 mediates foraging for leucine-enriched diets in <i>C. elegans</i>.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

MATLAB · 79 lines · 2.6 KB · no license

  1. clc; clear all; close all;
  2. %% location C:\';
  3. loc = [''];
  4. border = 110;
  5. IMthresh = 1.020; % 1.0-1.1
  7. %% Video export location
  8. v = VideoReader(loc);
  9. NumberFrame = v.NumFrames;
  11. newFileLoc = strcat(loc(1:end-4),'_tracking.avi');
  12. newFileLoc2 = strcat(loc(1:end-4),'_CropVideo.avi');
  13. v2 = VideoWriter(newFileLoc,'Motion JPEG AVI');
  14. v3 = VideoWriter(newFileLoc2,'Motion JPEG AVI');
  15. v2.Quality = 95;
  16. v3.Quality = 95;
  17. open(v2);
  18. open(v3);
  20. for i = 1:NumberFrame
  22. %% read frames
  23. frame = read(v,i);
  24. currentimage = im2double(rgb2gray(frame));
  25. if i == 1
  26. %% crop extra part
  27. [l,B] = size(currentimage);
  28. % currentimage = imcrop(currentimage,[1,40,B,1-40]);
  29. im56 = imbinarize(currentimage,0.09); % chage here if not working
  30. im56_BW = bwareaopen(im56,500);
  31. im56_BW_fil = imfill(im56_BW,'holes');
  32. % big blob identification
  33. [labeledImage, numberOfBlobs] = bwlabel(im56_BW_fil);
  34. blobMeasurements = regionprops(labeledImage, 'area');
  35. % Get all the areas
  36. allAreas = [blobMeasurements.Area];
  37. [sortedAreas, sortIndexes] = sort(allAreas, 'descend');
  38. biggestBlob = ismember(labeledImage, sortIndexes(1:1));
  39. % Convert from integer labeled image into binary (logical) image.
  40. binaryImage = biggestBlob > 0;
  41. stats = regionprops(binaryImage,'Centroid','MajorAxisLength','MinorAxisLength');
  42. centers = stats.Centroid;
  43. Center_X = floor(centers(1));
  44. Center_y = round(centers(2));
  45. radii = round((stats.MajorAxisLength+stats.MinorAxisLength)*0.25)- border;
  46. theta = linspace(0, 2*pi, round(4*pi*radii)); % Define angles
  47. % Get x and y vectors for each point along the circumference.
  48. x = radii * cos(theta) + Center_X;
  49. y = radii * sin(theta) + Center_y;
  50. myImage = zeros(size(currentimage));
  51. for k = 1:length(x)
  52. row = round(y(k));
  53. col = round(x(k));
  54. myImage(row, col) = 1;
  55. end
  56. myImage_BW_fil = imfill(myImage,'holes');
  57. end
  59. Final_image = currentimage.*myImage_BW_fil;
  60. I = imcrop(Final_image,[Center_X-radii,Center_y-radii,radii*2,radii*2]);
  62. %% noise reduction
  63. se = strel('disk',10);
  64. Io = imopen(I,se);
  65. Ie = imerode(I,se);
  66. Iobr = imreconstruct(Ie,I);
  67. Ioc = imclose(Io,se);
  68. Iobrd = imdilate(Iobr,se);
  69. Iobrcbr = imreconstruct(imcomplement(Iobrd),imcomplement(Iobr));
  70. I45 = I + Iobrcbr;
  71. fgm = I45>IMthresh;
  72. fgm3 = im2double(bwareaopen(fgm,5));
  73. writeVideo(v2,fgm3);
  74. writeVideo(v3,I)
  75. % imshow(fgm3,[]);
  76. % pause(0.1);
  77. end
  78. close(v2);
  79. close(v3);

Supplementary File 6.m, no license · at the source

Overview

Authors: Ritika Siddiqui1, Nikita Mehta1, Gopika Ranjith2, Marie-Anne Félix3, Changchun Chen4, Varsha Singh1,2
ORCID iDs: Ritika Siddiqui, Nikita Mehta, Gopika Ranjith, Changchun Chen, Varsha Singh
  1. Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
  2. Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
  3. Institute of Biology of the Ecole Normale Supérieure, Paris, France
  4. Department of Molecular Biology, Umeå University, Umeå, Sweden
Institutions: University of Dundee (United Kingdom); Indian Institute of Science Bangalore (India); École Normale Supérieure - PSL (France); Institut de Biologie de l'École Normale Supérieure (France); Umeå University (Sweden)
Journal: eLife, volume 13, article RP101936
Dates: published online 24 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.7554/elife.101936 · PMID 42029136 · PMCID PMC13108967 · OpenAlex W4403186680
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: C. elegans (organism), cellular / molecular (subfield)
Methods: Statistics, Evoked potentials, Smoothing, state filtering, decompositions
Keywords: C. elegans
MeSH: Caenorhabditis elegans*, Caenorhabditis elegans Proteins*, Diet*, Feeding Behavior*, Leucine*, Olfactory Receptor Neurons*, Receptors, Odorant*, Animals, Odorants, Pentanols (* major topic)
Topic: Genetics, Aging, and Longevity in Model Organisms (Aging, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Indo French Centre for Advanced Scientific Research (IFCP/6503-4); DBT/Wellcome Trust India Alliance (IA/S/21/1/505655); Royal Society (RSWF\R1\231005)
Citations: not cited yet (Europe PMC); 99 references in the paper

Abstract

Acquisition of essential nutrients through diet is crucial for the survival of animals. Dietary odors might enable animals to forage for nutrient-rich diets. We asked if Caenorhabditis elegans, a bacterivorous nematode, uses olfactory cues to forage for essential amino acid-rich (EAA) diets. Using the native microbiota of C. elegans, we show that worms rely on olfaction to select leucine (EAA)-supplemented bacteria. Using gas chromatography, we find that leucine-supplemented bacteria produce isoamyl alcohol (IAA) odor in the highest abundance. Prior adaptation of worms to IAA diminishes the diet preference of worms. Several wild isolates of C. elegans display robust responses to IAA, emphasizing its ecological relevance. We find that foraging for a leucine-supplemented diet is mediated via the AWC olfactory neurons. Finally, we identify SNIF-1 G protein-coupled receptor in AWC neurons as a receptor for IAA and a mediator of dietary decisions in worms. Our study identifies a receptor-ligand module underpinning foraging behavior in C. elegans.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

supp:PMC13108967/elife-101936-code1.zip

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Languages: MATLAB (1)
Size: 1 file, 1 script
Software Heritage: not checked
Found in: the supplementary material
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Image Processing Toolbox (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
1 file
At the source: pmc-oa-opendata.s3.amazonaws.com/PMC13108967.1/elife-101936-code1.zip

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1 script, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

Source data has been provided.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 6 authors, 1 keyword, 10 MeSH terms, 3 funders, 98 references.

Cite

This paper

Siddiqui, R., Mehta, N., Ranjith, G., Félix, M.-A., Chen, C., & Singh, V. (2026). The olfactory receptor SNIF-1 mediates foraging for leucine-enriched diets in <i>C. elegans</i>. eLife, 13, RP101936. https://doi.org/10.7554/elife.101936

BibTeX

@article{siddiqui2026olfactory,
author = {Siddiqui, Ritika and Mehta, Nikita and Ranjith, Gopika and Félix, Marie-Anne and Chen, Changchun and Singh, Varsha},
title = {{The olfactory receptor SNIF-1 mediates foraging for leucine-enriched diets in \<i\>C. elegans\</i\>}},
journal = {eLife},
year = {2026},
month = apr,
volume = {13},
pages = {RP101936},
publisher = {eLife Sciences Publications, Ltd},
issn = {2050-084X},
doi = {10.7554/elife.101936},
url = {https://doi.org/10.7554/elife.101936},
pmid = {42029136},
pmcid = {PMC13108967}
}

RIS

TY - JOUR
AU - Siddiqui, Ritika
AU - Mehta, Nikita
AU - Ranjith, Gopika
AU - Félix, Marie-Anne
AU - Chen, Changchun
AU - Singh, Varsha
TI - The olfactory receptor SNIF-1 mediates foraging for leucine-enriched diets in <i>C. elegans</i>
T2 - eLife
J2 - Elife
PY - 2026
DA - 2026/04/24
VL - 13
SP - RP101936
SN - 2050-084X
PB - eLife Sciences Publications, Ltd
DO - 10.7554/elife.101936
UR - https://doi.org/10.7554/elife.101936
LA - en
ER -

CSL-JSON

{
"id": "10.7554/elife.101936",
"type": "article-journal",
"title": "The olfactory receptor SNIF-1 mediates foraging for leucine-enriched diets in <i>C. elegans</i>",
"container-title": "eLife",
"author": [
{
"family": "Siddiqui",
"given": "Ritika"
},
{
"family": "Mehta",
"given": "Nikita"
},
{
"family": "Ranjith",
"given": "Gopika"
},
{
"family": "Félix",
"given": "Marie-Anne"
},
{
"family": "Chen",
"given": "Changchun"
},
{
"family": "Singh",
"given": "Varsha"
}
],
"container-title-short": "Elife",
"volume": "13",
"page": "RP101936",
"DOI": "10.7554/elife.101936",
"PMID": "42029136",
"PMCID": "PMC13108967",
"ISSN": "2050-084X",
"publisher": "eLife Sciences Publications, Ltd",
"URL": "https://doi.org/10.7554/elife.101936",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
24
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41593-026-02257-5 [code]
Neural sequences underlying directed turning in Caenorhabditis elegans.
Journal: Nature neuroscience
In common: C. elegans, 4 references
[2] doi:10.1038/s42003-026-10188-x
FLP-15 functions through the GPCR NPR-3 to regulate local and global search behaviours in Caenorhabditis elegans.
Journal: Communications biology
In common: C. elegans, cellular / molecular, 3 references
[3] doi:10.1371/journal.pcbi.1014152 [code]
Synchronization properties in C. elegans: Relating behavioral circuits to structural and functional neuronal connectivity.
Journal: PLoS computational biology
In common: C. elegans, 3 references
[4] doi:10.7554/elife.108675 [code]
SynaptoTagMe, a toolkit for in vivo mapping and modulating neurotransmission at single-cell resolution.
Journal: eLife
In common: C. elegans, cellular / molecular, 3 references
[5] doi:10.7554/elife.106496
AFD thermosensory neurons mediate tactile-dependent locomotion modulation in <i>C. elegans</i>.
Journal: eLife
In common: C. elegans, cellular / molecular, 2 references
[6] doi:10.1523/eneuro.0430-25.2026
Altered <i>glr-1</i> Expression after EtOH Withdrawal Is Linked to Associative Behavior Deficits in <i>C. elegans</i>.
Journal: eNeuro
In common: C. elegans, cellular / molecular, 2 references
[7] doi:10.3390/biom16070992
Molecular Networks and Key Regulators Underlying Resilience of the Human Brain to Aging and Dementia.
Journal: Biomolecules
In common: C. elegans, cellular / molecular, 1 reference
[8] doi:10.1038/s41586-026-10348-3 [code]
An enteric neuron ionotropic receptor regulates salt stress resistance.
Journal: Nature
In common: C. elegans, cellular / molecular, 1 reference
[9] doi:10.1016/j.isci.2026.117309 [code]
Intracellular regulation of a serotonin-gated ion channel links receptor trafficking to memory.
Journal: iScience
In common: C. elegans, cellular / molecular, 1 reference
[10] doi:10.1038/s41598-026-54384-5
Optimization of connectome weights for a neural network model generating both forward and backward locomotion in C. elegans.
Journal: Scientific reports
In common: C. elegans, 1 reference

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.