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Natural noncoding <i>pumilio</i> variants retune value-coding interneurons to bias <i>Drosophila</i> oviposition decisions.

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Paper

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

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The authors' code

Python · 108 lines · 3.7 KB · CC-BY-4.0

  1. from dotenv import load_dotenv
  2. from flask import Flask
  3. from flask_dance.contrib.google import make_google_blueprint
  4. from flask_login import LoginManager
  5. from flask_session import Session
  6. from flask_socketio import SocketIO
  7. from flask_sqlalchemy import SQLAlchemy
  8. import os
  9. import warnings
  11. from project.lib.datamanagement.sql_backend_types import SQLBackendTypes
  12. from project.lib.web.backend_types import BackendTypes
  15. SOCKETIO_POLLING_ONLY = os.getenv("SOCKETIO_POLLING_ONLY", "1") == "1"
  17. class ReverseProxied(object):
  18. def __init__(self, app):
  19. self.app = app
  21. def __call__(self, environ, start_response):
  22. scheme = environ.get("HTTP_X_FORWARDED_PROTO")
  23. if scheme:
  24. environ["wsgi.url_scheme"] = scheme
  25. return self.app(environ, start_response)
  28. load_dotenv()
  29. db = SQLAlchemy()
  30. app = Flask(__name__)
  31. app.wsgi_app = ReverseProxied(app.wsgi_app)
  32. login_manager = LoginManager()
  33. backend_type = BackendTypes[os.getenv("EGG_COUNTING_BACKEND_TYPE")]
  34. sql_addr_type = SQLBackendTypes[os.getenv("SQL_ADDR_TYPE")]
  35. if backend_type == BackendTypes.sql:
  36. if sql_addr_type == SQLBackendTypes.shortname:
  37. sql_addr = (
  38. f"mysql://root:{os.environ['GOOGLE_SQL_DB_PASSWORD']}@"
  39. f"/data?unix_socket=/cloudsql/{os.environ['GOOGLE_SQL_CONN_NAME']}"
  40. )
  41. elif sql_addr_type == SQLBackendTypes.ip_addr:
  42. sql_addr = (
  43. f"mysql://root:{os.environ['GOOGLE_SQL_DB_PASSWORD']}@"
  44. f"{os.environ['GOOGLE_SQL_DB_PVT_IP']}/data"
  45. )
  46. elif sql_addr_type == SQLBackendTypes.sqlite:
  47. sql_addr = "sqlite:///db.sqlite"
  48. flask_session_type = "sqlalchemy"
  49. elif backend_type == BackendTypes.filesystem:
  50. flask_session_type = "filesystem"
  51. app.config["BACKEND_TYPE"] = backend_type
  52. app.config["SQLALCHEMY_DATABASE_URI"] = sql_addr
  53. app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False
  54. db.init_app(app)
  55. app.config["SESSION_TYPE"] = flask_session_type
  56. session = Session(app)
  57. if flask_session_type == "sqlalchemy":
  58. with app.app_context():
  59. session.app.session_interface.db.create_all()
  60. socketio_kwargs = dict(manage_session=False)
  61. if SOCKETIO_POLLING_ONLY:
  62. socketio_kwargs.update(transports=['polling'], allow_upgrades=False)
  63. socketIO = SocketIO(app, **socketio_kwargs)
  65. sessions = {}
  66. UPLOAD_FOLDER = "./uploads"
  67. ALLOWED_EXTENSIONS = {"png", "jpg", "jpeg", "gif", "tif"}
  70. def create_app():
  71. warnings.filterwarnings("ignore", category=DeprecationWarning)
  72. warnings.filterwarnings(
  73. "default",
  74. message="OpenBLAS WARNING - could not determine the L2 cache size on"
  75. + " this system, assuming 256k",
  76. )
  77. os.environ["OAUTHLIB_INSECURE_TRANSPORT"] = "1"
  78. os.environ["OAUTHLIB_RELAX_TOKEN_SCOPE"] = "1"
  79. app.config["UPLOAD_FOLDER"] = UPLOAD_FOLDER
  80. app.google_client_id = os.getenv("GOOGLE_CLIENT_ID")
  81. app.google_client_secret = os.getenv("GOOGLE_CLIENT_SECRET")
  82. app.secret_key = os.getenv("SECRET_KEY")
  83. login_manager.login_view = "auth.login"
  84. login_manager.init_app(app)
  86. from .lib.datamanagement.models import User
  88. @login_manager.user_loader
  89. def load_user(user_id):
  90. return User.query.get(int(user_id))
  92. app.socketIO = socketIO
  93. from project.routes.auth import auth as auth_blueprint
  94. from project.routes.main import main as main_blueprint
  95. from project.routes.tasks import tasks as tasks_blueprint
  97. google_blueprint = make_google_blueprint(
  98. client_id=app.google_client_id,
  99. client_secret=app.google_client_secret,
  100. reprompt_consent=True,
  101. scope=["profile", "email"],
  102. )
  104. app.register_blueprint(main_blueprint)
  105. app.register_blueprint(auth_blueprint)
  106. app.register_blueprint(tasks_blueprint)
  107. app.register_blueprint(google_blueprint, url_prefix="/login")
  108. return app

__init__.py, under CC-BY-4.0 · at the source

Overview

Authors: Dorsa Motevalli1, Robert Alfredson1, Sydney Fogleman1, Emmanuel Medrano1, Yang Chen1, William I Silander2,3,4, Toshihide Hige2,3,4, Ulrich Stern1, Chung-Hui Yang1
ORCID iDs: Dorsa Motevalli, Robert Alfredson, Sydney Fogleman, Emmanuel Medrano, Yang Chen, William I Silander, Toshihide Hige, Ulrich Stern, Chung-Hui Yang
  1. Dept. of Neurobiology, Duke University Medical School, Durham, NC 27710, USA
  2. Dept. of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
  3. Dept. of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA
  4. Integrative Program for Biological and Genome Science, University of North Carolina, Chapel Hill, NC 27599, USA
Institutions: Duke University (United States); Duke Medical Center (United States); University of North Carolina at Chapel Hill (United States)
Journal: Science advances, volume 12, issue 19, article eaed1338
Dates: received 15 October 2025; accepted 6 April 2026; published online 8 May 2026; in print May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1126/sciadv.aed1338 · PMID 42102200 · PMCID PMC13155294 · OpenAlex W7160697979
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: drosophila (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Evoked potentials, fMRI & imaging, Single-unit activity, calcium imaging
MeSH: Drosophila*, Drosophila melanogaster*, Drosophila Proteins*, Interneurons*, Oviposition*, RNA-Binding Proteins*, Animals, Female, Polymorphism, Single Nucleotide, Sodium Channels (* major topic)
Topic: Neurobiology and Insect Physiology Research (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: Invertebrate Neuroscience Research Grant; National Science Foundation (2034783); National Institute on Deafness and Other Communication Disorders (R01DC018874)
Citations: not cited yet (Europe PMC); 42 references in the paper

Abstract

How natural regulatory genetic variation creates innate biases in economic decisions through modifying circuit structure and function is rarely explored. Here, we trace this link in a simple value-based decision in Drosophila: where to oviposit. Although laboratory flies (w1118) reject sucrose for a plain option, a wild-caught African strain accepts sucrose. This decision difference maps to three African-specific intronic SNPs in pumilio (pum), an RNA binding translational repressor. These SNPs down-regulate pum, derepressing its target, the sodium channel paralytic (para), in a pair of GABAergic interneurons that encode option value. Elevated para boosts neuronal excitability, compresses value contrast between sucrose and plain options, and promotes sucrose acceptance. Selectively reducing pum or overexpressing para in these neurons converts the laboratory flies’ physiology and behavior to the African phenotype. These findings offer a genome-to-circuit-to-behavior framework, revealing how subtle regulatory polymorphisms fine-tune circuit properties to diversify environment-appropriate decision biases in nature.

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

Repositories

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

Zenodo 18839001

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the text, “Egg-laying assay (standard)”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (22 files), OpenCV (11 files), PyTorch (10 files), Pillow (5 files), SciPy (5 files), scikit-image (3 files), Matplotlib (2 files), scikit-learn (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
68 files
At the source: doi.org/10.5281/zenodo.18839001

rcalfredson/eggsactly

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 5c66e1b47c055b99913bc7967e2584782dbf346c, 3 March 2026
Languages: Python (60), Shell (6), JavaScript (1)
Size: 117 files, 67 scripts
Software Heritage: not archived
Found in: the Zenodo archive record
Holds: README, environment (Dockerfile, environment.cuda11.0.yml, environment.cuda11.6.yml, requirements.3.13.txt, requirements.3.9.txt), tests, documentation
Not found: license file, CITATION.cff, continuous integration
Tools: NumPy (22 files), OpenCV (11 files), PyTorch (10 files), Pillow (5 files), SciPy (5 files), scikit-image (3 files), Matplotlib (2 files), scikit-learn (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
68 files, not copied: shown from their source

OSCR keeps no copy of these files: this repository has no license that allows it. The reader above shows each one from its source, fetched by your browser at commit 5c66e1b, when its fingerprint is the one OSCR verified. How this works.

At the source: github.com/rcalfredson/Eggsactly/tree/1.0.1

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

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 134 scripts, 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, code, and materials availability

All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplemental Materials. Details for how to synthesize materials or access specific repositories are in the Materials and Methods section. Raw traces can be found here: https://doi.org/10.5281/zenodo.18836685.

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

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 10 MeSH terms, 3 funders, 42 references.

Cite

This paper

Motevalli, D., Alfredson, R., Fogleman, S., Medrano, E., Chen, Y., Silander, W. I., Hige, T., Stern, U., & Yang, C.-H. (2026). Natural noncoding <i>pumilio</i> variants retune value-coding interneurons to bias <i>Drosophila</i> oviposition decisions. Science advances, 12(19), eaed1338. https://doi.org/10.1126/sciadv.aed1338

BibTeX

@article{motevalli2026natural,
author = {Motevalli, Dorsa and Alfredson, Robert and Fogleman, Sydney and Medrano, Emmanuel and Chen, Yang and Silander, William I and Hige, Toshihide and Stern, Ulrich and Yang, Chung-Hui},
title = {{Natural noncoding \<i\>pumilio\</i\> variants retune value-coding interneurons to bias \<i\>Drosophila\</i\> oviposition decisions}},
journal = {Science advances},
year = {2026},
month = may,
volume = {12},
number = {19},
pages = {eaed1338},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
doi = {10.1126/sciadv.aed1338},
url = {https://doi.org/10.1126/sciadv.aed1338},
pmid = {42102200},
pmcid = {PMC13155294}
}

RIS

TY - JOUR
AU - Motevalli, Dorsa
AU - Alfredson, Robert
AU - Fogleman, Sydney
AU - Medrano, Emmanuel
AU - Chen, Yang
AU - Silander, William I
AU - Hige, Toshihide
AU - Stern, Ulrich
AU - Yang, Chung-Hui
TI - Natural noncoding <i>pumilio</i> variants retune value-coding interneurons to bias <i>Drosophila</i> oviposition decisions
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/05/08
VL - 12
IS - 19
SP - eaed1338
SN - 2375-2548
PB - American Association for the Advancement of Science
DO - 10.1126/sciadv.aed1338
UR - https://doi.org/10.1126/sciadv.aed1338
LA - en
ER -

CSL-JSON

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"container-title": "Science advances",
"author": [
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