Avian arcopallium
Ontology highlight
ABSTRACT:
ORGANISM(S): Coturnix japonica Calypte anna Melopsittacus undulatus Taeniopygia guttata Streptopelia risoria
PROVIDER: GSE28395 | GEO | 2011/11/30
SECONDARY ACCESSION(S): PRJNA139189
REPOSITORIES: GEO
Similar Datasets
Project description:To determine what kind of genes are involved in vocal learning ability, we performed microarray experiments using 3 vocal learning species (zebra finch, budgerigar, Anna's hummingbird) and 2 non-vocal learning species(ring dive, and Japanese quail) from the bird group. All of the animals are male adults. They were isolated over night and had 1hour light exposure at morning. Birds who did not sing were used in this experiment.
2012-05-31 | GSE33667 | GEO
Project description:To determine what kind of genes are involved in vocal learning ability, we performed microarray experiments using 3 vocal learning species (zebra finch, budgerigar, Anna's hummingbird) and 2 non-vocal learning species(ring dive, and Japanese quail) from bird group. All of the animals are adult males. They were isolated over night and had 1hour light exposure at morning. Birds who did not sing were used in this experiment. We used 2-3 animals each species. We use arcopallium song nucleus for vocal learners and intermediate arcopallium for non-vocal learners. We used surrounding arcopallium as control area for both groups.
2011-11-30 | E-GEOD-28395 | biostudies-arrayexpress
Project description:To determine what kind of genes are involved in vocal learning ability, we performed microarray experiments using 3 vocal learning species (zebra finch, budgerigar, Anna's hummingbird) and 2 non-vocal learning species(ring dive, and Japanese quail) from the bird group. All of the animals are male adults. They were isolated over night and had 1hour light exposure at morning. Birds who did not sing were used in this experiment. We used 2-3 animals each species. We used the 12th motor neuron for both vocal learners and non-vocal learners. We used the Supra Spinal motor neuron (ssp) as control area for both groups.
2012-05-30 | E-GEOD-33667 | biostudies-arrayexpress
Project description:We applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis, formerly Taeniopygia guttata castanotis), a Neoaves songbird species and a common model of vocal learning.
2024-04-16 | GSE264042 | GEO
Project description:Primordial germ cells (PGCs), major cell resource used in the production of germline chimeras in birds, have been used in conservation of avian genetic resources and production of transgenic animals. Numerous bird species have been put on the brink of extinction due to habitat loss and degradation caused by environmental destruction and climate change, but research on PGCs is limited to specific poultry, such as chickens. Although it has recently been expanding to various bird species, it is still difficult to utilize PGCs due to biological differences and difficulties in in vitro long-term culture. Here, we constructed a single-cell landscape of chicken gonadal PGCs with established long-term culture systems of PGCs and compared them with those of the vocal learning wild bird, the zebra finches. Our results identified the interspecific differences in signaling pathways in gonadal PGCs and somatic cells, respectively. In particular, the NODAL and insulin signaling pathways were more active in zebra finch than in chickens, whereas the FGF downstream signaling pathway known to be important for the proliferation of chicken PGCs, was more active in chickens. These differences may contribute to optimizing the in vitro culture conditions of zebra finch PGCs. This study is the first cross-species single-cell transcriptomic analysis targeting birds, and laid an essential groundwork to contribute to the restoration of endangered birds and the production of transgenic birds by securing sufficient PGCs from various bird species in the future.
2023-11-28 | GSE208178 | GEO
Project description:Similarities between speech and birdsong make songbirds advantageous for investigating the neurogenetics of learned vocal communication; a complex phenotype likely supported by ensembles of interacting genes in cortico-basal ganglia pathways of both species. To date, only FoxP2 has been identified as critical to both speech and birdsong. We performed weighted gene co-expression network analysis on microarray data from singing zebra finches to discover gene ensembles regulated during vocal behavior. We found ~2,000 singing- regulated genes comprising 3 co-expression groups unique to area X, the basal ganglia subregion dedicated to learned vocal-motor behavior. These contained known targets of human FOXP2 and potential avian targets. We validated novel biological pathways for vocalization. Our findings show that higher-order gene co-expression patterns, rather than expression levels, molecularly distinguish area X from the ventral striato-pallidum during singing. The previously unknown structure of singing-driven networks enables prioritization of molecular interactors that likely bear on human motor disorders, especially those affecting speech. Gene expression was measured in 2 basal ganglia sub-regions (area X & ventral striato-pallidum (VSP)) of 27 adult male zebra finches that sang different amounts of song over a 2hr period in the morning. 18 birds were allowed to sing freely, 9 birds were discouraged from singing by the presence of an investigator and those that sang fewer than 10 song motifs were considered “non-singers”.
2012-01-04 | E-GEOD-34819 | biostudies-arrayexpress
Project description:Vocal learning and neuronal replacement have been studied extensively in the songbird brain, but until recently, few molecular and genomic tools have been available for this work. Here we describe new molecular/genomic resources for songbird research. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11000 clones were sequenced from these libraries, representing 5870 unique gene transcripts. A web-based database has been established for sequence analysis and functional annotations. The cDNA libraries were not normalized. Sequence analysis revealed that a cDNA library made from brains at post-hatching day 30-50, when the song system goes through rapid development and birds learn to sing, shows the highest gene discovery rate. We grouped genes into functional categories according to the Gene Ontology classification and found that expression of the functional categories changed as the brain developed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the HVC of both adult male zebra finches and canaries (Serinus canaria). Statistical Analysis of Microarrays (SAM) was used for data analysis. A subset of the differentially regulated genes was validated by in situ hybridization. The bioinformatic tools EASE and Ingenuity Pathway Analysis were used to identify over-represented functional groups and gene networks among the regulated genes. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis. Keywords: HVC, songbird, cDNA microarray, gene expression
2006-12-06 | GSE6412 | GEO
Project description:Like human speech, birdsong is a complex vocal behavior that is acquired by sensorimotor learning based on coordination of auditory input and vocal output to mimic memorized tutor song. Here we investigate neural circuits for vocal learning and production in deafened songbirds to elucidate how sensory-input regulate genetic and epigenetic property of vocal development and its associated gene expression dynamics. Compared with audition-intact birds, in deafened zebra finches, the vocal development is delayed but song crystallization is observed at more than three times later, producing individually different but structured vocal patterns. In contrast to the distinct difference of vocal ontogeny between audition (+) and (-), unexpectedly, developmental regulation of gene expression dynamics is strictly conserved with age-locked trend in vocal motor circuit in both intact and deafened birds, indicating sensory-input independent robustness of developmental gene expression dynamics in the motor circuit for sensorimotor learning. This discrepancy between outward vocal phenotype and inward gene expression dynamics provides new insight into neural regulation at closing of the critical period for vocal learning by two different forms: auditory inputs-dependent M-bM-^@M-^XactiveM-bM-^@M-^Y crystallization and gene expression dynamics-mediated M-bM-^@M-^XpassiveM-bM-^@M-^Y crystallization. We collected brain samples from intact and early-deafened birds (deafened at day-post hatch 17-23) under silent and dark condition. Song nuclei in vocal motor circuit, HVC and RA tissue samples (juvenile; n = 3, young; n = 3, old; n = 3 of intact and early-deafened birds for HVC and RA) were laser-microdissected from total 24 birds (intact; n = 12, early-deafened; n = 12). Each sample was hybridized to a single array, totaling 36 arrays. Birds were selected per slide such that early-deafened birds were paired with intact birds. To minimize possible interslide bias or batch effects, intact and early-deafened bird samples matching with brain area and age conditions were hybridized side by side on same array glass.
2014-03-21 | E-GEOD-56075 | biostudies-arrayexpress
Project description:The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line from zebra finch embryonic fibroblasts using the SV40 large and small T antigens, designated CFS414. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. This single-cell RNA sequencing experiment provided information on the gene expression landscape of the cell line, informing on its cell type, transcriptomic stability, and value to researchers utilizing the zebra finch as a model organism.
2022-02-04 | GSE195934 | GEO
Project description:Human speech is one of the few examples of vocal learning among mammals, yet ~half of avian species exhibit this ability. Its genetic basis is unknown beyond a shared requirement for FoxP2 in both humans and zebra finches. Here we manipulated FoxP2 isoforms in Area X during a critical period for song development, delineating, for the first time, unique contributions of each to vocal learning. We used weighted gene coexpression network analysis of RNA-seq data to construct transcriptional profiles and found gene modules correlated to singing, learning, or vocal variability. The juvenile song modules were preserved adults, whereas the learning modules were not. The learning modules were preserved in the striatopallidum adjacent to Area X whereas the song modules were not. The confluence of learning and singing coexpression in juvenile, but not adult, Area X may underscore molecular processes that drive vocal learning in zebra finches and, by analogy, humans.
2018-01-25 | GSE96843 | GEO