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Manfred Gahr - One of the best experts on this subject based on the ideXlab platform.

  • the genome of blue capped cordon bleu uncovers hidden diversity of ltr retrotransposons in Zebra Finch
    Genes, 2019
    Co-Authors: Jesper Boman, Carolina Franklvilches, Michelly Dos S Santos, Edivaldo Herculano Correa De Oliveira, Manfred Gahr
    Abstract:

    Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In Zebra Finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from Zebra Finch at the root of estrildid Finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the Zebra Finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in Zebra Finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.

  • individual recognition of opposite sex vocalizations in the Zebra Finch
    Scientific Reports, 2017
    Co-Authors: Pietro B Damelio, Manfred Gahr, Milena Klumb, Mauricio Nicolas Adreani, Andries Ter Maat
    Abstract:

    Individual vocal recognition plays an important role in the social lives of many vocally active species. In group-living songbirds the most common vocalizations during communal interactions are low-intensity, soft, unlearned calls. Being able to tell individuals apart solely from a short call would allow a sender to choose a specific group member to address, resulting in the possibility to form complex communication networks. However, little research has yet been carried out to discover whether soft calls contain individual identity. In this study, males and females of Zebra Finch pairs were tested with six vocalization types - four different soft calls, the distance call and the male song - to investigate whether they are able to distinguish individuals of the opposite sex. For both sexes, we provide the first evidence of individual vocal recognition for a Zebra Finch soft unlearned call. Moreover, while controlling for habituation and testing for repeatability of the findings, we quantify the effects of hitherto little studied variables such as partners’ vocal exchange previous to the experiment, spectral content of playback calls and quality of the answers. We suggest that Zebra Finches can recognize individuals via soft vocalizations, therefore allowing complex directed communication within vocalizing flocks.

  • comparative cytogenetics between two important songbird models the Zebra Finch and the canary
    PLOS ONE, 2017
    Co-Authors: Michelly Dos S Santos, Carolina Franklvilches, Antje Bakker, Patricia C M O Brien, Rafael Kretschmer, Malcolm A Fergusonsmith, Manfred Gahr, Edivaldo Herculano Correa De Oliveira
    Abstract:

    Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the Zebra Finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both Zebra Finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the Zebra Finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1.

  • Horizontal transmission of the father's song in the Zebra Finch (Taeniopygia guttata).
    Biology Letters, 2013
    Co-Authors: Sébastien Derégnaucourt, Manfred Gahr
    Abstract:

    As is the case for human speech, birdsong is transmitted across generations by imitative learning. Although transfer of song patterns from adults to juveniles typically occurs via vertical or oblique transmission, there is also evidence of horizontal transmission between juveniles of the same generation. Here, we show that a young male Zebra Finch (Taeniopygia guttata) that has been exposed to its father during the sensitive period for song learning can lead a brother, that has never heard the paternal song, to imitate some sounds of the father. Moreover, song similarity between the two brothers was higher than the similarity measured between the paternal song and the song of the brother that had a week-long exposure to the father. We speculate that the phenomenon of within-generation song learning among juveniles may be more widespread than previously thought and that when a juvenile evaluates potential models for imitative learning, a sibling may be as salient as an adult.

  • comparisons of different methods to train a young Zebra Finch taeniopygia guttata to learn a song
    Journal of Physiology-paris, 2013
    Co-Authors: Sébastien Derégnaucourt, Colline Poirier, Anne Van Der Kant, Annemie Van Der Linden, Manfred Gahr
    Abstract:

    Like humans, oscine songbirds exhibit vocal learning. They learn their song by imitating conspecifics, mainly adults. Among them, the Zebra Finch (Taeniopygia guttata) has been widely used as a model species to study the behavioral, cellular and molecular substrates of vocal learning. Various methods using taped song playback have been used in the laboratory to train young male Finches to learn a song. Since different protocols have been applied by different research groups, the efficiency of the studies cannot be directly compared. The purpose of our study was to address this problem. Young Finches were raised by their mother alone from day post hatching (dph) 10 and singly isolated from dph 35. One week later, exposure to a song model began, either using a live tutor or taped playback (passive or self-elicited). At dph 100, the birds were transferred to a common aviary. We observed that one-to-one live tutoring is the best method to get a fairly complete imitation. Using self-elicited playback we observed high inter-individual variability; while some Finches learned well (including good copying of the song model), others exhibited poor copying. Passive playback resulted in poor imitation of the model. We also observed that Finches exhibited vocal changes after dph 100 and that the range of these changes was negatively related to their imitation of the song model. Taken together, these results suggest that social aspects are predominant in the success outcome of song learning in the Zebra Finch.

Barney A Schlinger - One of the best experts on this subject based on the ideXlab platform.

  • the stressed brain regional and stress related corticosterone and stress regulated gene expression in the adult Zebra Finch taeniopygia guttata
    Journal of Neuroendocrinology, 2020
    Co-Authors: Michelle A Rensel, Barney A Schlinger
    Abstract:

    Glucocorticoids (CORT) are well-known as important regulators of behaviour and cognition at basal levels and under stress. However, the precise mechanisms governing CORT action and functional outcomes of this action in the brain remain unclear, particularly in model systems other than rodents. In the present study, we investigated the dynamics of CORT regulation in the Zebra Finch, an important model system for vocal learning, neuroplasticity and cognition. We tested the hypothesis that CORT is locally regulated in the Zebra Finch brain by quantifying regional and stress-related variation in total CORT across brain regions. In addition, we used an ex vivo slice culture system to test whether CORT regulates target gene expression uniquely in discrete regions of the brain. We documented a robust increase in brain CORT across regions after 30 minutes of restraint stress but, interestingly, baseline and stress-induced CORT levels varied between regions. In addition, CORT treatment of brain slice cultures differentially affected expression of three CORT target genes: it up-regulated expression of FKBP5 in most regions and SGK1 in the hypothalamus only, whereas GILZ was unaffected by CORT treatment across all brain regions investigated. The specific mechanisms producing regional variation in CORT and CORT-dependent downstream gene expression remain unknown, although these data provide additional support for the hypothesis that the songbird brain employs regulatory mechanisms that result in precise control over the influence of CORT on glucocorticoid-sensitive neural circuits.

  • Rapid Upregulation of Aromatase mRNA and Protein Following Neural Injury in the Zebra Finch (Taeniopygia guttata)
    Journal of neuroendocrinology, 2001
    Co-Authors: R. Scott Peterson, Colin J Saldanha, Barney A Schlinger
    Abstract:

    The expression of aromatase (oestrogen synthase) within the vertebrate central nervous system (CNS) is key in the provision of local oestrogens to neural circuits. Aromatase expression appears to be exclusively neuronal under normal conditions. However, some in vitro studies suggest the presence of astrocytic aromatase in songbirds and mammals. Recently, aromatase in reactive astrocytes has been demonstrated in response to neural injury in the mammalian CNS. Since the glial aromatase expression first documented in cultures of the songbird telencephalon may reflect processes similar to those in response to mammalian neural injury, we investigated whether injury alters the pattern of aromatase-expression in the Zebra Finch, a species with very high levels of forebrain aromatase expression. Adult males received a penetrating neural injury to the right hemisphere and were killed either 24 or 72 h later. Controls were anaesthetized and otherwise unmanipulated. We determined the expression of aromatase mRNA and protein using in situ hybridization and immunocytochemistry, respectively. Both the transcription and translation of aromatase is dramatically upregulated around the lesion site in response to neural injury in the Zebra Finch forebrain. This effect is robust and rapid, occurring within 24 h of the injury itself. Cells that upregulate aromatase appear to be reactive astrocytes based upon morphology. The hemisphere contralateral to the injury and both hemispheres in control birds showed the normal, exclusively neuronal pattern of aromatase expression. The upregulation of aromatase in astrocytes may provide high levels of oestrogen available to modulate processes such as CNS repair. Injury-induced upregulation of astrocytic aromatase may be a general characteristic of the injured vertebrate brain.

  • distribution and regulation of telencephalic aromatase expression in the Zebra Finch revealed with a specific antibody
    The Journal of Comparative Neurology, 2000
    Co-Authors: Colin J Saldanha, Arthur P. Arnold, Melanie J Tuerk, Augustine O Fernandes, Barney A Schlinger
    Abstract:

    In songbirds, aromatase (estrogen synthase) activity and mRNA are readily detectable in the brain. This neural aromatization presumably provides estrogen to steroid-sensitive targets via autocrine, paracrine, and synaptic mechanisms. The location of immunoreactive protein, however, has been difficult to describe completely, particularly in distal dendrites, axons, and terminals of the forebrain. Here we describe the neuroanatomical distribution of aromatase in the Zebra Finch by using a novel antibody raised specifically against Zebra Finch aromatase. The distribution of aromatase-positive somata in the Zebra Finch brain is in excellent agreement with previous reports. Additionally, this antibody reveals elaborate, spinous dendritic arbors, fine-beaded axons, and punctate terminals of telencephalic neurons that may synthesize estrogen. Some of these axon-like fibers extend into the high vocal center (HVC) and the robust nucleus of the archistriatum (RA) in males and females, suggesting a role for presynaptic aromatization in cellular processes within these loci. Adult males have more aromatase-positive fibers in the caudomedial neostriatum (NCM) and the preoptic area (POA) compared to females, despite the lack of detectable sex differences in the number of immunoreactive somata at these loci. Thus, the compartmentalization of aromatase in dendrites and axons may serve a sexually dimorphic function in the songbird. Finally, in adult males, aromatase expression is down-regulated by circulating estradiol in the hippocampus, but not in the NCM or POA. The distribution of aromatase suggests a role for aromatization in the regulation of pre- and postsynaptic function in steroid sensitive areas of the songbird forebrain. J. Comp. Neurol. 423:619–630, 2000. © 2000 Wiley-Liss, Inc.

  • distribution and regulation of telencephalic aromatase expression in the Zebra Finch revealed with a specific antibody
    The Journal of Comparative Neurology, 2000
    Co-Authors: Colin J Saldanha, Arthur P. Arnold, Melanie J Tuerk, Yonghwan Kim, Augustine Fernandes, Barney A Schlinger
    Abstract:

    In songbirds, aromatase (estrogen synthase) activity and mRNA are readily detectable in the brain. This neural aromatization presumably provides estrogen to steroid-sensitive targets via autocrine, paracrine, and synaptic mechanisms. The location of immunoreactive protein, however, has been difficult to describe completely, particularly in distal dendrites, axons, and terminals of the forebrain. Here we describe the neuroanatomical distribution of aromatase in the Zebra Finch by using a novel antibody raised specifically against Zebra Finch aromatase. The distribution of aromatase-positive somata in the Zebra Finch brain is in excellent agreement with previous reports. Additionally, this antibody reveals elaborate, spinous dendritic arbors, fine-beaded axons, and punctate terminals of telencephalic neurons that may synthesize estrogen. Some of these axon-like fibers extend into the high vocal center (HVC) and the robust nucleus of the archistriatum (RA) in males and females, suggesting a role for presynaptic aromatization in cellular processes within these loci. Adult males have more aromatase-positive fibers in the caudomedial neostriatum (NCM) and the preoptic area (POA) compared to females, despite the lack of detectable sex differences in the number of immunoreactive somata at these loci. Thus, the compartmentalization of aromatase in dendrites and axons may serve a sexually dimorphic function in the songbird. Finally, in adult males, aromatase expression is down-regulated by circulating estradiol in the hippocampus, but not in the NCM or POA. The distribution of aromatase suggests a role for aromatization in the regulation of pre- and postsynaptic function in steroid sensitive areas of the songbird forebrain.

Carolina Franklvilches - One of the best experts on this subject based on the ideXlab platform.

  • dna methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in Zebra Finch telencephalon
    Frontiers in Cell and Developmental Biology, 2021
    Co-Authors: Jolien Diddens, Sandra Steyaert, Ellen De Meester, Sarah De Keulenaer, Carolina Franklvilches, Jeroen Galle, Louis Coussement, Gaurav Majumdar, Sita M Ter Haar, Wim Van Criekinge
    Abstract:

    Song learning in Zebra Finches (Taeniopygia guttata) is a prototypical example of a complex learned behavior, yet knowledge of the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA-sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched Zebra Finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing Zebra Finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age-dependent gene expression was found for various transcription factors (i.e., OTX2, AR, and FOS) involved in neurodevelopment. Incomplete dosage compensation, independent of DNA methylation, was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in Zebra Finch telencephalon.

  • the genome of blue capped cordon bleu uncovers hidden diversity of ltr retrotransposons in Zebra Finch
    Genes, 2019
    Co-Authors: Jesper Boman, Carolina Franklvilches, Michelly Dos S Santos, Edivaldo Herculano Correa De Oliveira, Manfred Gahr
    Abstract:

    Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In Zebra Finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from Zebra Finch at the root of estrildid Finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the Zebra Finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in Zebra Finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.

  • comparative cytogenetics between two important songbird models the Zebra Finch and the canary
    PLOS ONE, 2017
    Co-Authors: Michelly Dos S Santos, Carolina Franklvilches, Antje Bakker, Patricia C M O Brien, Rafael Kretschmer, Malcolm A Fergusonsmith, Manfred Gahr, Edivaldo Herculano Correa De Oliveira
    Abstract:

    Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the Zebra Finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both Zebra Finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the Zebra Finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1.

  • a genome wide search for epigenetically regulated genes in Zebra Finch using methylcap seq and rna seq
    Scientific Reports, 2016
    Co-Authors: Sandra Steyaert, Jolien Diddens, Ellen De Meester, Sarah De Keulenaer, Nina Sohniuswilhelmi, Carolina Franklvilches, Antje Bakker, Annemarie Van Der Linden, Jeroen Galle, Wim Van Criekinge
    Abstract:

    Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the Zebra Finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two Zebra Finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in Zebra Finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the Zebra Finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.

Jon Slate - One of the best experts on this subject based on the ideXlab platform.

  • red carotenoid coloration in the Zebra Finch is controlled by a cytochrome p450 gene cluster
    Current Biology, 2016
    Co-Authors: Nicholas I Mundy, Jessica Stapley, Terry Burke, T R Birkhead, Clair Bennison, Rachel Tucker, Hanlu Twyman, Kangwook Kim, Staffan Andersson, Jon Slate
    Abstract:

    Bright-red colors in vertebrates are commonly involved in sexual, social, and interspecific signaling [1-8] and are largely produced by ketocarotenoid pigments. In land birds, ketocarotenoids such as astaxanthin are usually metabolically derived via ketolation of dietary yellow carotenoids [9, 10]. However, the molecular basis of this gene-environment mechanism has remained obscure. Here we use the yellowbeak mutation in the Zebra Finch (Taeniopygia guttata) to investigate the genetic basis of red coloration. Wild-type ketocarotenoids were absent in the beak and tarsus of yellowbeak birds. The yellowbeak mutation mapped to chromosome 8, close to a cluster of cytochrome P450 loci (CYP2J2-like) that are candidates for carotenoid ketolases. The wild-type Zebra Finch genome was found to have three intact genes in this cluster: CYP2J19A, CYP2J19B, and CYP2J40. In yellowbeak, there are multiple mutations: loss of a complete CYP2J19 gene, a modified remaining CYP2J19 gene (CYP2J19(yb)), and a non-synonymous SNP in CYP2J40. In wild-type birds, CYP2J19 loci are expressed in ketocarotenoid-containing tissues: CYP2J19A only in the retina and CYP2J19B in the beak and tarsus and to a variable extent in the retina. In contrast, expression of CYP2J19(yb) is barely detectable in the beak of yellowbeak birds. CYP2J40 has broad tissue expression and shows no differences between wild-type and yellowbeak. Our results indicate that CYP2J19 genes are strong candidates for the carotenoid ketolase and imply that ketolation occurs in the integument in Zebra Finches. Since cytochrome P450 enzymes include key detoxification enzymes, our results raise the intriguing possibility that red coloration may be an honest signal of detoxification ability.

  • Genetic mapping of the major histocompatibility complex in the Zebra Finch (Taeniopygia guttata)
    Immunogenetics, 2011
    Co-Authors: Robert Ekblom, Jessica Stapley, Terry Burke, Alex D. Ball, Tim Birkhead, Jon Slate
    Abstract:

    Genes of the major histocompatibility complex (MHC) have received much attention in immunology, genetics, and ecology because they are highly polymorphic and play important roles in parasite resistance and mate choice. Until recently, the MHC of passerine birds was not well-described. However, the genome sequencing of the Zebra Finch ( Taeniopygia guttata ) has partially redressed this gap in our knowledge of avian MHC genes. Here, we contribute further to the understanding of the Zebra Finch MHC organization by mapping SNPs within or close to known MHC genes in the Zebra Finch genome. MHC class I and IIB genes were both mapped to Zebra Finch chromosome 16, and there was no evidence that MHC class I genes are located on chromosome 22 (as suggested by the genome assembly). We confirm the location in the MHC region on chromosome 16 for several other genes (BRD2, FLOT1, TRIM7.2, GNB2L1, and CSNK2B). Two of these (CSNK2B and FLOT1) have not previously been mapped in any other bird species. In line with previous results, we also find that orthologs to the immune-related genes B-NK and CLEC2D, which are part of the MHC region in chicken, are situated on Zebra Finch chromosome Z and not among other MHC genes in the Zebra Finch.

  • a comparison of snps and microsatellites as linkage mapping markers lessons from the Zebra Finch taeniopygia guttata
    BMC Genomics, 2010
    Co-Authors: A. H. Ball, Jessica Stapley, Deborah A Dawson, Terry Burke, Tim R. Birkhead, Jon Slate
    Abstract:

    Background Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four Zebra Finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled Zebra Finch genome sequence.

  • digital gene expression analysis of the Zebra Finch genome
    BMC Genomics, 2010
    Co-Authors: Robert Ekblom, Christopher N. Balakrishnan, Terry Burke, Jon Slate
    Abstract:

    Background In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the Zebra Finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC).

  • a comparison of snps and microsatellites as linkage mapping markers lessons from the Zebra Finch taeniopygia guttata
    BMC Genomics, 2010
    Co-Authors: Alexander Ball, Jessica Stapley, Deborah A Dawson, Terry Burke, T R Birkhead, Jon Slate
    Abstract:

    Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four Zebra Finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled Zebra Finch genome sequence. We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy. When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable.

Colin J Saldanha - One of the best experts on this subject based on the ideXlab platform.

  • discovery of the first germline restricted gene by subtractive transcriptomic analysis in the Zebra Finch taeniopygia guttata
    Current Biology, 2018
    Co-Authors: Michelle K Biederman, Megan M Nelson, Kathryn C Asalone, Alyssa L Pedersen, Colin J Saldanha, John R Bracht
    Abstract:

    Summary Developmentally programmed genome rearrangements are rare in vertebrates, but have been reported in scattered lineages including the bandicoot, hagfish, lamprey, and Zebra Finch ( Taeniopygia guttata ) [1]. In the Finch, a well-studied animal model for neuroendocrinology and vocal learning [2], one such programmed genome rearrangement involves a germline-restricted chromosome, or GRC, which is found in germlines of both sexes but eliminated from mature sperm [3, 4]. Transmitted only through the oocyte, it displays uniparental female-driven inheritance, and early in embryonic development is apparently eliminated from all somatic tissue in both sexes [3, 4]. The GRC comprises the longest Finch chromosome at over 120 million base pairs [3], and previously the only known GRC-derived sequence was repetitive and non-coding [5]. Because the Zebra Finch genome project was sourced from male muscle (somatic) tissue [6], the remaining genomic sequence and protein-coding content of the GRC remain unknown. Here we report the first protein-coding gene from the GRC: a member of the α-soluble N- ethylmaleimide sensitive fusion protein (NSF) attachment protein (α-SNAP) family hitherto missing from Zebra Finch gene annotations. In addition to the GRC-encoded α-SNAP, we find an additional paralogous α-SNAP residing in the somatic genome (a somatolog)—making the Zebra Finch the first example in which α-SNAP is not a single-copy gene. We show divergent, sex-biased expression for the paralogs and also that positive selection is detectable across the bird α-SNAP lineage, including the GRC-encoded α-SNAP. This study presents the identification and evolutionary characterization of the first protein-coding GRC gene in any organism.

  • Rapid Upregulation of Aromatase mRNA and Protein Following Neural Injury in the Zebra Finch (Taeniopygia guttata)
    Journal of neuroendocrinology, 2001
    Co-Authors: R. Scott Peterson, Colin J Saldanha, Barney A Schlinger
    Abstract:

    The expression of aromatase (oestrogen synthase) within the vertebrate central nervous system (CNS) is key in the provision of local oestrogens to neural circuits. Aromatase expression appears to be exclusively neuronal under normal conditions. However, some in vitro studies suggest the presence of astrocytic aromatase in songbirds and mammals. Recently, aromatase in reactive astrocytes has been demonstrated in response to neural injury in the mammalian CNS. Since the glial aromatase expression first documented in cultures of the songbird telencephalon may reflect processes similar to those in response to mammalian neural injury, we investigated whether injury alters the pattern of aromatase-expression in the Zebra Finch, a species with very high levels of forebrain aromatase expression. Adult males received a penetrating neural injury to the right hemisphere and were killed either 24 or 72 h later. Controls were anaesthetized and otherwise unmanipulated. We determined the expression of aromatase mRNA and protein using in situ hybridization and immunocytochemistry, respectively. Both the transcription and translation of aromatase is dramatically upregulated around the lesion site in response to neural injury in the Zebra Finch forebrain. This effect is robust and rapid, occurring within 24 h of the injury itself. Cells that upregulate aromatase appear to be reactive astrocytes based upon morphology. The hemisphere contralateral to the injury and both hemispheres in control birds showed the normal, exclusively neuronal pattern of aromatase expression. The upregulation of aromatase in astrocytes may provide high levels of oestrogen available to modulate processes such as CNS repair. Injury-induced upregulation of astrocytic aromatase may be a general characteristic of the injured vertebrate brain.

  • distribution and regulation of telencephalic aromatase expression in the Zebra Finch revealed with a specific antibody
    The Journal of Comparative Neurology, 2000
    Co-Authors: Colin J Saldanha, Arthur P. Arnold, Melanie J Tuerk, Augustine O Fernandes, Barney A Schlinger
    Abstract:

    In songbirds, aromatase (estrogen synthase) activity and mRNA are readily detectable in the brain. This neural aromatization presumably provides estrogen to steroid-sensitive targets via autocrine, paracrine, and synaptic mechanisms. The location of immunoreactive protein, however, has been difficult to describe completely, particularly in distal dendrites, axons, and terminals of the forebrain. Here we describe the neuroanatomical distribution of aromatase in the Zebra Finch by using a novel antibody raised specifically against Zebra Finch aromatase. The distribution of aromatase-positive somata in the Zebra Finch brain is in excellent agreement with previous reports. Additionally, this antibody reveals elaborate, spinous dendritic arbors, fine-beaded axons, and punctate terminals of telencephalic neurons that may synthesize estrogen. Some of these axon-like fibers extend into the high vocal center (HVC) and the robust nucleus of the archistriatum (RA) in males and females, suggesting a role for presynaptic aromatization in cellular processes within these loci. Adult males have more aromatase-positive fibers in the caudomedial neostriatum (NCM) and the preoptic area (POA) compared to females, despite the lack of detectable sex differences in the number of immunoreactive somata at these loci. Thus, the compartmentalization of aromatase in dendrites and axons may serve a sexually dimorphic function in the songbird. Finally, in adult males, aromatase expression is down-regulated by circulating estradiol in the hippocampus, but not in the NCM or POA. The distribution of aromatase suggests a role for aromatization in the regulation of pre- and postsynaptic function in steroid sensitive areas of the songbird forebrain. J. Comp. Neurol. 423:619–630, 2000. © 2000 Wiley-Liss, Inc.

  • distribution and regulation of telencephalic aromatase expression in the Zebra Finch revealed with a specific antibody
    The Journal of Comparative Neurology, 2000
    Co-Authors: Colin J Saldanha, Arthur P. Arnold, Melanie J Tuerk, Yonghwan Kim, Augustine Fernandes, Barney A Schlinger
    Abstract:

    In songbirds, aromatase (estrogen synthase) activity and mRNA are readily detectable in the brain. This neural aromatization presumably provides estrogen to steroid-sensitive targets via autocrine, paracrine, and synaptic mechanisms. The location of immunoreactive protein, however, has been difficult to describe completely, particularly in distal dendrites, axons, and terminals of the forebrain. Here we describe the neuroanatomical distribution of aromatase in the Zebra Finch by using a novel antibody raised specifically against Zebra Finch aromatase. The distribution of aromatase-positive somata in the Zebra Finch brain is in excellent agreement with previous reports. Additionally, this antibody reveals elaborate, spinous dendritic arbors, fine-beaded axons, and punctate terminals of telencephalic neurons that may synthesize estrogen. Some of these axon-like fibers extend into the high vocal center (HVC) and the robust nucleus of the archistriatum (RA) in males and females, suggesting a role for presynaptic aromatization in cellular processes within these loci. Adult males have more aromatase-positive fibers in the caudomedial neostriatum (NCM) and the preoptic area (POA) compared to females, despite the lack of detectable sex differences in the number of immunoreactive somata at these loci. Thus, the compartmentalization of aromatase in dendrites and axons may serve a sexually dimorphic function in the songbird. Finally, in adult males, aromatase expression is down-regulated by circulating estradiol in the hippocampus, but not in the NCM or POA. The distribution of aromatase suggests a role for aromatization in the regulation of pre- and postsynaptic function in steroid sensitive areas of the songbird forebrain.