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Glutamatergic projections from the substantia nigra pars reticulata to the dorsal raphe nucleus regulate male social hierarchies.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § Results › Chemogenetic inhibition of SNrGlu neurons results in defeat in the tube test ↔ Matlab_code_for_line_charts.m, lines 44–56 · score 0.59 · post CNO injection, Behavioral annotation, push initiation, EGFP mice, pre, hM4Di
  2. [2] § Materials and methods › Behavioral tests › Tube test. ↔ Matlab_code_for_line_charts.m, lines 44–56 · score 0.50 · behavioral annotation, push initiation, resistance, stillness, retreat, tube

Paper

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

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The authors' code

MATLAB · 58 lines · 5.4 KB · CC-BY-4.0 · 2 matches

  1. %%% This code is designed for visualizing rank changes and annotating behavioral observations in the tube test.
  3. clear all
  4. close all
  5. clc
  7. %%% Plot for social rank changes for a cohort of hM4Di-EGFP mice before and after CNO administration to the rank-3 mouse at time 0.
  8. rankchange=[1 1 1 1 1 3 1 1 1 %% Creat a sample data for rankchange
  9. 4 4 4 4 4 4 4 4 4
  10. 2 2 2 2 2 1 2 2 2
  11. 3 3 3 3 3 2 3 3 3];
  12. rankchange=5-rankchange;
  13. figure(1)
  14. subplot(2,2,1)
  15. plot(rankchange(1,:),'-sm','MarkerFaceColor','m','LineWidth',2);hold on;
  16. plot(rankchange(2,:),'-s','Color',[0.5 0.5 0.5],'MarkerFaceColor',[0.5 0.5 0.5],'LineWidth',2);hold on;
  17. plot(rankchange(3,:),'-s','Color',[0.5 0.5 0.5],'MarkerFaceColor',[0.5 0.5 0.5],'LineWidth',2);hold on;
  18. plot(rankchange(4,:),'-s','Color',[0.5 0.5 0.5],'MarkerFaceColor',[0.5 0.5 0.5],'LineWidth',2);hold on;axis([0 10 0.5 4.5]);
  19. % xticklabel_rotate([1:9],45,{'-72','-48','-24','0','1-1.5','6-8','24','48','72'},'interpreter','none'); text(9.5,0.2,'(hr)');set(gca,'linewidth',1);
  21. %%%% Plot for mean change in rank prior to and following injection of CNO or saline
  22. [hM4Di_CNO_s11,hM4Di_CNO_s12,hM4Di_CNO_s13]=xlsread('Social_rank_changes_hM4Di.xlsx','hM4Di_EYFP_CNO_RC'); %% Read data
  23. [hM4Di_Saline_s11,hM4Di_Saline_s12,hM4Di_Saline_s13]=xlsread('Social_rank_changes_hM4Di.xlsx','hM4Di_EYFP_Saline_RC');
  24. [EYFP_CNO_s11,EYFP_CNO_s12,EYFP_CNO_s13]=xlsread('Social_rank_changes_hM4Di.xlsx','EYFP_CNO_RC');
  25. mean_hM4Di_CNO=mean(hM4Di_CNO_s11(:,2:end));std_hM4Di_CNO=std(hM4Di_CNO_s11(:,2:end))/sqrt(length(mean_hM4Di_CNO(:,2:end)));
  26. mean_hM4Di_Saline=mean(hM4Di_Saline_s11(:,2:end));std_hM4Di_Saline=std(hM4Di_Saline_s11(:,2:end))/sqrt(length(mean_hM4Di_Saline(:,2:end)));
  27. mean_EYFP_CNO=mean(EYFP_CNO_s11(:,2:end));std_EYFP_CNO=std(EYFP_CNO_s11(:,2:end))/sqrt(length(mean_EYFP_CNO(:,2:end)));
  28. subplot(2,2,3)
  29. plot(mean_hM4Di_Saline+0.4,'-s','Color',[0.5 0.5 0.5],'MarkerFaceColor',[0.5 0.5 0.5],'LineWidth',2);hold on;
  30. plot(mean_EYFP_CNO+0.2,'-s','Color',[255 165 0]/256,'MarkerFaceColor',[255 165 0]/256,'LineWidth',2);hold on;axis([0 10 -2 1]);
  31. plot(mean_hM4Di_CNO,'-sm','MarkerFaceColor','m','LineWidth',2);errorbar(mean_hM4Di_CNO,std_hM4Di_CNO,'m','LineWidth',2);hold on;
  32. % xticklabel_rotate([1:9],45,{'-72','-48','-24','0','1-1.5','6-8','24','48','72'},'interpreter','none'); text(9.5,-2.2,'(hr)');set(gca,'linewidth',1);legend('hM4Di+Saline','EYFP+CNO','hM4Di+CNO')
  35. %%%% Plot for summary of rank changes in hM4Di-EGFP mice following CNO administration to each individual at time 0.
  36. x=ones(1,9);y=1:9;
  37. hM4Di_CNO_s11_1=fliplr(hM4Di_CNO_s11(:,2:end));
  38. subplot(2,2,2)
  39. plot3(x,y,hM4Di_CNO_s11_1(6,:),'Color',[255 20 147]/256,'LineWidth',2);hold on;plot3(x+1,y,hM4Di_CNO_s11_1(2,:),'Color',[255 0 255]/256,'LineWidth',2);hold on;plot3(x+2,y,hM4Di_CNO_s11_1(3,:),'Color',[138 43 226]/256,'LineWidth',2);hold on;
  40. plot3(x+3,y,hM4Di_CNO_s11_1(4,:),'Color',[46 139 87]/256,'LineWidth',2);hold on;plot3(x+4,y,hM4Di_CNO_s11_1(5,:),'Color',[173 255 47]/256,'LineWidth',2);hold on;plot3(x+5,y,hM4Di_CNO_s11_1(1,:),'Color',[255 215 0]/256,'LineWidth',2);hold on;
  41. plot3(x+6,y,hM4Di_CNO_s11_1(7,:),'Color',[255 140 0]/256,'LineWidth',2);hold on;plot3(x+7,y,hM4Di_CNO_s11_1(8,:),'Color',[124 252 0]/256,'LineWidth',2);hold on;plot3(x+8,y,hM4Di_CNO_s11_1(9,:),'Color',[0 250 154]/256,'LineWidth',2);hold on;set(gca,'linewidth',1);
  42. plot3(y,x+5,x-1,'--','Color',[128 0 0]/256,'LineWidth',1);axis([0 9 0 10 -2 1]);
  44. %%%% Plot for behavioral annotation of two tube test trials between the same pair of hM4Di-EGFP mice, pre- and post-CNO injection.
  45. x1=[13.033 15.1 19.1]-13.033; y1=[4 4 4]+2; %% stillness, push initiation
  46. x2=[13.033 15.1 18.5 19.1]-13.033; y2=[3 3 3 3]+2; %% stillness, resistance, retreat
  47. x3=[10.033 12.5 13.033 15.1 15.767 15.967 18.233]-10.033; y3=[2 2 2 2 2 2 2]; %% resistance, push back, stillness, resistance, push back, retreat
  48. x4=[10.033 12.5 13.033 13.433 15.167 15.833 15.967 18.233]-10.033; y4=[2 2 2 2 2 2 2 2]-1; %% push initiation, resistance, retreat, stillness, push initiation, resistance, push back
  49. subplot(2,2,4)
  50. plot(x1(1:2),y1(1:2),'Color',[192 192 192]/256,'LineWidth',12);hold on; plot(x1(2:3),y1(2:3),'Color',[255 0 0]/256,'LineWidth',12);hold on;
  51. plot(x2(1:2),y2(1:2),'Color',[192 192 192]/256,'LineWidth',12);hold on; plot(x2(2:3),y2(2:3),'Color',[255 215 0]/256,'LineWidth',12);hold on; plot(x2(3:4),y2(3:4),'Color',[0 191 255]/256,'LineWidth',12);hold on;
  52. plot(x3(1:2),y3(1:2),'Color',[255 215 0]/256,'LineWidth',12);hold on; plot(x3(2:3),y3(2:3),'Color',[255 105 180]/256,'LineWidth',12);hold on; plot(x3(3:4),y3(3:4),'Color',[192 192 192]/256,'LineWidth',12);hold on;
  53. plot(x3(4:5),y3(4:5),'Color',[255 215 0]/256,'LineWidth',12);hold on; plot(x3(5:6),y3(5:6),'Color',[255 105 180]/256,'LineWidth',12);hold on; plot(x3(6:7),y3(6:7),'Color',[0 191 255]/256,'LineWidth',12);hold on;
  54. plot(x4(1:2),y4(1:2),'Color',[255 0 0]/256,'LineWidth',12);hold on; plot(x4(2:3),y4(2:3),'Color',[255 215 0]/256,'LineWidth',12);hold on; plot(x4(3:4),y4(3:4),'Color',[0 191 255]/256,'LineWidth',12);hold on;
  55. plot(x4(4:5),y4(4:5),'Color',[192 192 192]/256,'LineWidth',12);hold on; plot(x4(5:6),y4(5:6),'Color',[255 0 0]/256,'LineWidth',12);hold on; plot(x4(6:7),y4(6:7),'Color',[255 215 0]/256,'LineWidth',12);hold on;plot(x4(7:8),y4(7:8),'Color',[255 105 180]/256,'LineWidth',12);hold on;
  56. axis([0 9 0 7]);xlabel('Time from meeting (s)'); legend('Stillness','push initiation','Resistance','Retreat','Push back');

Matlab_code_for_line_charts.m, under CC-BY-4.0 · at the source

Overview

Authors: Yanzhu Fan1, Shaoxiang Ge1,2, Lidi Lu1, Wenjun Niu1, Zhiyue Wang1, Xiaoguo Jiao2, Guangzhan Fang1
ORCID iDs: Guangzhan Fang
  1. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
  2. School of Life Sciences, Hubei University, Wuhan, Hubei, China
Institutions: Chinese Academy of Sciences (China); Chengdu Institute of Biology (China); Hubei University (China)
Journal: PLoS biology, volume 24, issue 3, article e3003687
Dates: received 11 April 2025; accepted 19 February 2026; published online 3 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pbio.3003687 · PMID 41774700 · PMCID PMC12974815 · OpenAlex W7133317516
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), systems (subfield)
Methods: Statistics, Preprocessing, Single-unit activity, calcium imaging
MeSH: Dorsal Raphe Nucleus*, Glutamic Acid*, Hierarchy, Social*, Pars Reticulata*, Substantia Nigra*, Animals, Male, Mice, Mice, Inbred C57BL, Neural Pathways, Neurons, Optogenetics, Social Dominance (* major topic)
Topic: Neuroendocrine regulation and behavior (Social Psychology, Psychology), according to OpenAlex
Funding: National Natural Science Foundation of China (32170504, 221100210500); Natural Science Foundation of Sichuan Province (2026NSFSC0920)
Citations: cited by 1 paper (Europe PMC); 98 references in the paper

Abstract

Social hierarchy constitutes a fundamental organizational characteristic among various social species, significantly influencing individual survival, health, and reproductive success within these societies. Neurons in the substantia nigra pars reticulata (SNr) exhibit extensive connectivity with the dorsal raphe nucleus (DRN), a critical structure implicated in social interaction, reward processing, and the establishment of social rank. However, the specific neuronal types within the SNr, as well as the associated neural circuits that regulate social dominance, remain inadequately characterized. This study aims to elucidate the crucial role of SNr glutamatergic (SNrGlu) neurons in the establishment and maintenance of social hierarchy in male mice. Employing fiber photometry, we observed that the activation of SNrGlu neurons increased during the initiation of effortful behaviors in the tube test. Further investigations revealed that optogenetic activation or chemogenetic inhibition of the SNrGlu neurons induced upward or downward shifts in social ranks, respectively. Additionally, our findings indicate that the activation of SNr glutamatergic terminals in DRN elevates social status and reduces anxiety levels in mice. Collectively, these results broaden our understanding of the functions associated with SNrGlu neurons and underscore their critical role in regulating social hierarchy among male mice. This work enhances our understanding of the functions of SNrGlu neurons in both physiological contexts and neurological disorders.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

Zenodo 18618228

License: CC-BY-4.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Languages: R (2), MATLAB (1)
Size: 3 files, 3 scripts
Software Heritage: not checked
Found in: “Data Availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (2 files), tidyverse (2 files), car (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
3 files
At the source: doi.org/10.5281/zenodo.18618228

The paper's code and data availability statement is in the Data section.

Tracing map

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  • 3 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Data

Datasets cited

Data Availability

The dataset generated and analyzed during the current study is available in the Dryad repository: https://doi.org/10.5061/dryad.m0cfxppg3. Furthermore, the scripts for data visualization are accessible in the Zenodo repository: https://doi.org/10.5281/zenodo.18618228.

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, issue, pages, dates, 7 authors, 13 MeSH terms, 2 funders, 96 references.

Cite

This paper

Fan, Y., Ge, S., Lu, L., Niu, W., Wang, Z., Jiao, X., & Fang, G. (2026). Glutamatergic projections from the substantia nigra pars reticulata to the dorsal raphe nucleus regulate male social hierarchies. PLoS biology, 24(3), e3003687. https://doi.org/10.1371/journal.pbio.3003687

BibTeX

@article{fan2026glutamatergic,
author = {Fan, Yanzhu and Ge, Shaoxiang and Lu, Lidi and Niu, Wenjun and Wang, Zhiyue and Jiao, Xiaoguo and Fang, Guangzhan},
title = {{Glutamatergic projections from the substantia nigra pars reticulata to the dorsal raphe nucleus regulate male social hierarchies}},
journal = {PLoS biology},
year = {2026},
month = mar,
volume = {24},
number = {3},
pages = {e3003687},
publisher = {PLOS},
issn = {1544-9173},
doi = {10.1371/journal.pbio.3003687},
url = {https://doi.org/10.1371/journal.pbio.3003687},
pmid = {41774700},
pmcid = {PMC12974815}
}

RIS

TY - JOUR
AU - Fan, Yanzhu
AU - Ge, Shaoxiang
AU - Lu, Lidi
AU - Niu, Wenjun
AU - Wang, Zhiyue
AU - Jiao, Xiaoguo
AU - Fang, Guangzhan
TI - Glutamatergic projections from the substantia nigra pars reticulata to the dorsal raphe nucleus regulate male social hierarchies
T2 - PLoS biology
J2 - PLoS Biol
PY - 2026
DA - 2026/03/03
VL - 24
IS - 3
SP - e3003687
SN - 1544-9173
PB - PLOS
DO - 10.1371/journal.pbio.3003687
UR - https://doi.org/10.1371/journal.pbio.3003687
LA - en
ER -

CSL-JSON

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"container-title": "PLoS biology",
"author": [
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3
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}

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