An innate fear response in domestic chicks: screening for short copy number variations associated with tonic immobility
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ABSTRACT:
ORGANISM(S): Gallus gallus
SUBMITTER: Hideaki Abe
PROVIDER: E-GEOD-38434 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We performed aCGH analysis among domestic chicks (Gallus gallus) with different sensitivity in the tonic immobility (TI) to identify the copy number aberrants within genes or regions responsible for innate fear responses.
2013-03-31 | GSE38434 | GEO
Project description:To uncover genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and genotype information, two gene co-expression networks correlated with context-dependent immobility were identified. We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling. We mapped 27 behavioral quantitative trait loci with a false discovery rate of 5%. We also identified two gene co-expression networks correlated with context-dependent immobility. Highly connected genes in the context fear modules included Psmd6, Ube2a and Usp33, suggesting an important role for ubiquitination in learning and memory. We surveyed the architecture of brain transcript regulation and showed preservation of gene co-expression modules in hippocampus and striatum while also highlighting important differences. Rps15a, Kif3a, Stard7, 6330503K22RIK, and Plvap were among the individual genes whose transcript abundance associated strongly with fear phenotypes.
2011-03-15 | GSE26500 | GEO
Project description:To uncover genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and genotype information, two gene co-expression networks correlated with context-dependent immobility were identified. We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling. We mapped 27 behavioral quantitative trait loci with a false discovery rate of 5%. We also identified two gene co-expression networks correlated with context-dependent immobility. Highly connected genes in the context fear modules included Psmd6, Ube2a and Usp33, suggesting an important role for ubiquitination in learning and memory. We surveyed the architecture of brain transcript regulation and showed preservation of gene co-expression modules in hippocampus and striatum while also highlighting important differences. Rps15a, Kif3a, Stard7, 6330503K22RIK, and Plvap were among the individual genes whose transcript abundance associated strongly with fear phenotypes. Total mRNA islolated from hippocampus and striatum of strains from Hybrid Mouse Diversity Panel and gene expression quantified using Illumina MouseRef-8 v2.0 microarrays. Submission includes gene expression data from 100 strains of HMDP for hippocampus (n=1 for each strain) and 98 strains of HMDP for striatum (n=1 for each strain).
2011-03-15 | E-GEOD-26500 | biostudies-arrayexpress
Project description:Newly-hatched domestic chick serves as an important model for studies of neural and behavioral plasticity, particularly with respect to learning and memory such as filial imprinting. Imprinting is assumed to be a unique case of recognition learning with some characteristic features, such as sensitive period and irreversibility. However, the molecules involved in the memory process are yet to be fully identified. To address this issue, we attempted to identify the genes differentially expressed at an earlier phase of filial imprinting than described in our previous report (Brain Res. Bull.76, 275-281 (2008)). One-day-old chicks were trained for imprinting for 1 h and whole brains were collected and used for cDNA microarray analysis and quantitative RT-PCR. We identified 18 genes upregulated accompanying filial imprinting. These results suggested that the increase of these 18 genes associated with filial imprinting might play an important role in the acquisition of memory in the filial imprinting. Total RNA was extracted from whole brains of trained chicks (n=16) and control dark-reared chicks (n=16). Using these total RNAs, we performed RT-PCR to distinguish male chicks from females. Then total RNAs were separated and mixed in four groups (1, male trained (n=8); 2, female trained (n=8); 3, male dark-reared (n=8); and 4, female dark-reared chicks (n=8)), and we performed cDNA microarray expression analysis to identify the upregulated genes following imprinting (1 versus 3 and 2 versus 4).
2012-08-20 | E-GEOD-31055 | biostudies-arrayexpress
Project description:Salmonella remains an important enteric pathogen of poultry, primarily due to concerns regarding food-borne illness in humans consuming contaminated poultry products. Specific probiotic cultures are efficacious as a treatment for neonatal poultry to prevent enteric infections (competitive exclusion) due to the exquisite susceptibility of young chicks to pathogens in the hatchery and brooding environment. The objective of this experiment was to analyze transcriptional profiles in the ceca of neonatal chicks using the Arizona Gallus gallus 20.7K Oligo Array v1.0, following treatment with a probiotic culture derived from poultry with and without Salmonella enterica subsp. Enteritidis (SE) challenge. Chicks were obtained from a commercial hatchery, and challenged with SE upon arrival at the laboratory. One hour post-challenge, chicks were treated with a probiotic culture (FM-B11). Treatment groups included: Control (no challenge or treatment, vehicle only), SE (challenged only), B11 (treated only) and SE+B11 (challenged and treated). Samples were obtained at 12h and 24h post-treatment. We observed that administration of a Lactobacillus-based probiotic culture to chicks following challenge with SE reduced SE colonization of the cecae and resulted in differential expression of genes in the cecae. Among all four treatment groups, 309 genes were differentially expressed (p<0.05) at 12h, and 352 genes were differentially expressed (p<0.05) at 24h. Keywords: disease state analysis
2010-01-14 | GSE19887 | GEO
Project description:Absence is a notion that is usually captured by language-related concepts like zero or negation. Whether nonlinguistic creatures encode similar thoughts is an open question, as everyday behavior marked by absence (of food, of social partners) can be explained solely by expecting presence somewhere else. We investigated 8-day-old chicks' looking behavior in response to events violating expectations about the presence or absence of an object. We found different behavioral responses to violations of presence and absence, suggesting distinct underlying mechanisms. Importantly, chicks displayed an avian signature of novelty detection to violations of absence, namely a sex-dependent left-eye-bias. Follow-up experiments excluded accounts that would explain this bias by perceptual mismatch or by representing the object at different locations. These results suggest that the ability to spontaneously form representations about the absence of objects likely belongs to the initial cognitive repertoire of vertebrate species.
| S-EPMC9000949 | biostudies-literature
Project description:Salmonella remains an important enteric pathogen of poultry, primarily due to concerns regarding food-borne illness in humans consuming contaminated poultry products. Specific probiotic cultures are efficacious as a treatment for neonatal poultry to prevent enteric infections (competitive exclusion) due to the exquisite susceptibility of young chicks to pathogens in the hatchery and brooding environment. The objective of this experiment was to analyze transcriptional profiles in the ceca of neonatal chicks using the Arizona Gallus gallus 20.7K Oligo Array v1.0, following treatment with a probiotic culture derived from poultry with and without Salmonella enterica subsp. Enteritidis (SE) challenge. Chicks were obtained from a commercial hatchery, and challenged with SE upon arrival at the laboratory. One hour post-challenge, chicks were treated with a probiotic culture (FM-B11). Treatment groups included: Control (no challenge or treatment, vehicle only), SE (challenged only), B11 (treated only) and SE+B11 (challenged and treated). Samples were obtained at 12h and 24h post-treatment. We observed that administration of a Lactobacillus-based probiotic culture to chicks following challenge with SE reduced SE colonization of the cecae and resulted in differential expression of genes in the cecae. Among all four treatment groups, 309 genes were differentially expressed (p<0.05) at 12h, and 352 genes were differentially expressed (p<0.05) at 24h. Keywords: disease state analysis Eight experimental groups with 4 replicates each were analyzed. A reference RNA design was used for this microarray. Equal amounts of amplified RNA (aRNA) from all samples were pooled and labelled with the Alexa 647 to create the reference pool. Each individual sample was labelled with Alexa 555. Each slide was hybridized with both the reference pool and one sample.
2010-05-15 | E-GEOD-19887 | biostudies-arrayexpress
Project description:Unlearned tendencies to approach animate creatures are of great adaptive value, especially for nidifugous social birds that need to react to the presence of potential social companions shortly after hatching. Domestic chicks' preferences for taxidermized hens provided the first evidence of social predispositions. However, the nature of the stimuli eliciting this predisposition is not completely understood. Here we explore the unlearned preferences of visually naïve domestic chicks for taxidermized animals. Visually naive chicks were tested for their approach preferences between a target stimulus (an intact stuffed animal whose head region was clearly visible) and a control stimulus. After confirming the predisposition for the intact stuffed fowl hen (Exp. 1), we found an analogous preference for a taxidermized, young domestic chick over a severely scrambled version of the same stimulus, whose body structure was completely disrupted, extending to same-age individuals the results that had been obtained with taxidermized hens (Exp. 2). We also directly tested preferences for specimens whose head region is visible compared to ones whose head region was occluded. To clarify whether chicks are sensitive to species-specific information, we employed specimens of female mallard ducks and of a mammalian predator, the polecat. Chicks showed a preference for the duck stimulus whose wings have been covered over a similar stimulus whose head region has been covered, providing direct evidence that the visibility of the head region of taxidermized models drive chicks' behaviour in this test, and that the attraction for the head region indeed extends to females of other bird species (Exp. 3). However, no similar preference was obtained with the polecat stimuli (Exp. 4). We thus confirmed the presence of unlearned visual preferences for the head region in newly-hatched chicks, though other factors can limit the species-generality of the phenomenon.
| S-EPMC6719852 | biostudies-literature
Project description:Gallus gallus breed:HuaiXiang Domestic Chickens Raw sequence reads
| PRJNA481097 | ENA
Project description:Gallus gallus breed:Kirin Domestic Chickens Raw sequence reads
| PRJNA481134 | ENA