DOI: 10.5061/dryad.6m905qgdf
title: Data from: Unpredictability and adaptive responses to dietary variability in Japanese quail

description: Understanding animals' molecular mechanisms of adaptation to
 unpredictable changes in dietary availability provides insights into how
 organisms optimize resource utilisation and ensure survival under such
 conditions. The mechanistic target of rapamycin (mTOR) is a candidate
 nutrient-sensing pathway underpinning a form of adaptive plasticity when
 individuals encounter constraints in their energy budget. We exposed adult
 Japanese quails (Coturnix japonica) of both sexes to three dietary
 conditions: daily unpredictable feeding, constant restriction, and full
 feeding for 16 days. Our study revealed that unpredictability reduced the
 body mass of female birds, whereas males remained unaffected. Egg
 production traits were not affected by unpredictable feeding. However,
 constant dietary restriction had a significant negative impact, suggesting
 resource reallocation to reproduction under unpredictable feeding
 conditions. We found sex-dependent gene expression patterns of mTOR
 pathway genes: while the unpredictable treatment did not affect gene
 expression in males, it downregulated MTOR and insulin-like growth
 factor-1 (IGF1) and its receptor (IGF1R), and upregulated Unc-51-like
 autophagy activating kinase-1 (ULK1) and autophagy-related genes (ATG9A,
 ATG5) in females. Additionally, variation in mTOR pathway gene expression
 was significantly associated with the effect of treatments on body mass
 and egg mass. Our study highlighted molecular mechanisms and adaptive
 responses towards dietary unpredictability and scarcity.
description: # Data from: Unpredictability and adaptive responses to dietary
 variability in Japanese quail Reda GK, Ndunguru SF, Csernus B, Knop R,
 Szabó C, Czeglédi L, Lendvai ÁZ: Unpredictability and adaptive responses
 to dietary variability in Japanese quail ## Description of the data and
 file structure The data consist of a set of files, including (1) Body mass
 of birds, (2) Egg number and egg mass, (3) gene expression, (4) Feed
 intake, (5) Pre-tratment body mass, (6) Pre-treatment feed intake, (7) R
 code used to generate all analyses and figures. ## Files and variables ###
 File 1: body_mass.xlsx **Description:** We exposed adult Japanese quails
 (Coturnix japonica) of both sexes to three dietary conditions: daily
 unpredictable feeding, 40% constant restriction, and full feeding for 16
 days. We measured body mass at the beginning of the experiment (day 0) and
 on days 4, 8, and 16 of the treatment period using a digital scale (± 0.1
 g). The unit of measurement was gram (g). The data contains 5 columns and
 193 rows. #### variables * birdID: bird identification number. *
 Treatment: different dietary regimens. * Sex: male and female birds. *
 Day; measurement day. * Mass: body mass in grams. * Control: full-fed
 group. * UNPR: Unpredictably fed group. * DR40; 40% restricted group. ###
 File 2: egg_mass_number.xlsx **Description:** We record egg-laying
 attendance and measure egg mass on a daily basis throughout the
 restriction period using a digital scale (± 0.01 g). The unit of
 measurement for egg mass was grams (g). Egg number was calculated from the
 number of records per bird in the restriction period. The data contains 4
 columns and 409 rows. #### variables * birdID: bird identification number.
 * Treatment: different dietary regimens. * Day, recording day. * egg_mass;
 egg mass in grams. * Control: full-fed group. * UNPR: Unpredictably fed
 group. * DR40; 40% restricted group. ### File 3: gene_expression.xlsx
 **Description:** To analyse mRNA relative expression, we used real-time
 quantitative PCR using EvaGreen qPCR Mix (Solis BioDyne, Teaduspargi,
 Estonia) according to the manufacturer’s protocol.  Intron-spanning
 gene-specific primer pairs for quails were designed using Oligo7 software
 and obtained from Integrated DNA Technologies (BVBA-Leuven, Belgium). 
 Among the most frequently used reference genes in birds, we selected the
 best-performing reference gene, ribosomal protein L19 (RPL19), using
 NormFinder, BestKeepe,r, and deltaCt algorithms.  The 2−ΔΔCt method was
 employed to analyze the relative changes in mRNA expression of target
 genes (IGF1, IGF1R, FOXO1, mTOR, RPS6K1, 4EBP1, ULK1, ATG9A, and ATG5).
 #### variables * birdI:; bird identification number. * Treatment:
 different dietary restriction levels. * Sex: male and female birds. *
 Tissue samples were collected from the liver and muscle. * IGF1;
 insulin-like growth factor 1 gene expression. * IGF1R; insulin-like growth
 factor 1 receptor gene expression. * FOXO1; Forkhead box O1 gene
 expression. * mTOR; mechanistic target of rapamycin gene expression. *
 RPS6K1; ribosomal protein S6 kinase 1 gene expression. * 4EBP1; eukaryotic
 translation initiation factor 4E-binding protein 1 gene expression. *
 ULK1: Unc-51-like autophagy activating kinase 1 gene expression. * ATG9A;
 autophagy-related 9A gene expression. * ATG5; autophagy-related 5 gene
 expression. * Control: full-fed group. * UNPR: Unpredictably fed group. *
 DR40; 40% restricted group. ### File 4: feed_intake.xlsx **Description:**
 Each morning, immediately after the lights turned on, we removed the
 feeders before birds began eating, weighed the remaining food using a
 digital scale with a precision of ±0.01 g. Then the daily feed intake (g)
 was calculated by subtracting the remaining food from the given food. ####
 variables * birdID: bird identification number. * Sex: male and female
 birds. * Treatment: different dietary regimens. * Day; measurement day. *
 Intake: daily feed intake of individual birds in grams. * Control:
 full-fed group. * UNPR: Unpredictably fed group. * DR40; 40% restricted
 group. ### File 5: pre_treatement_body_mass.xlsx **Description:** Prior to
 the application of actual treatment, the body mass of birds was measured
 during the immediate pre-treatment week. Body mass (g) was measured seven
 days and one day before the application of the experimental treatments,
 using a digital scale with a precision of ±0.1 g. This was used to assess
 if there is any body change. #### variables * birdI: bird identification
 number. * Sex: male or female birds. * Day: Days before the beginning of
 the application of the actual experiment. * Mass: body mass in grams. ###
 File 6: pre_treatment_intake.xlsx **Description:** Quails were provided ad
 libitum access to feed and water during the seven days preceding the start
 of the experiment while housed individually in cages .  These data were
 collected to determine the appropriate dietary level for each bird
 according to its assigned treatment group. Feed intake was measured every
 morning using a digital scale with a precision of ±0.1 g, and values were
 recorded in grams. #### variables * birdID: bird identification number. *
 Day; measurement day. * Sex: male and female. * Intake: daily feed intake
 of individual birds. ### File 7:
 R_script_for_data_anlysis_and_plotting.Rmd **Description:** R code used to
 generate all analyses and plotting figures is scripted in this file. ##
 Code/software Analyses were conducted in R (v4.5.1); the scripts in
 `R_script_for_data_anlysis_and_plotting.Rmd` reproduce all results.  Key
 packages included tidyverse, lme4/lmerTest, gamm4, aod, emmeans, ggplot2,
 ggcorrplot, multcompView, readxl, gridExtra, grid, factoextra, lavaan, and
 semPlot.