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54,099 results for “Expression”
Polybrominated diphenyl ethers in human follicular fluid dysregulate mural and cumulus granulosa cell gene expression
<p>Polybrominated diphenyl ethers (PBDEs), a major class of flame retardants incorporated into numerous consumer products, leach out into dust resulting in widespread exposure. There is evidence from <i>in vitro</i> and <i>in vivo</i> animal studies that PBDEs affect ovarian granulosa cell function and follicular development, yet human studies of their association with female infertility are inconclusive. Here, we tested the hypothesis that exposure to the PBDEs in follicular fluid is associated with dysregulation of gene expression in the mural and cumulus granulosa cells collected from women undergoing in vitro fertilization by intracytoplasmic sperm injection. The median concentration of the ∑<sub>10</sub>PBDEs detected in the follicular fluid samples (n=37) was 15.04 pg/g wet weight. RNA microarray analyses revealed that many genes were differentially expressed in mural and cumulus granulosa cells. Highest <i>vs</i>. lowest quartile exposure to the Σ<sub>10</sub>PBDEs or to two predominant PBDE congeners, BDE-47 or BDE-153, was associated with significant effects on gene expression in both cell types. Mural granulosa cells were generally more sensitive to PBDE exposure compared to cumulus cells. Overall, gene expression changes associated with BDE-47 exposure were similar to those for ∑<sub>10</sub>PBDEs but distinct from those associated with BDE-153 exposure. Interestingly, exposure to BDE-47 and ∑<sub>10</sub>PBDEs activated the expression of genes in pathways that are important in innate immunity and inflammation. To the best of our knowledge, this is the first demonstration that exposure to these environmental chemicals is associated with the dysregulation of pathways that play an essential role in ovulation.</p>
Tomato Plants Treated with Systemin Peptide Show Enhanced Levels of Direct and Indirect Defense Associated with Increased Expression of Defense-Related Genes
<p>Numerical data that underlies tables, graphs and statistics of the Plants article from Coppola et al., 2019: "Tomato Plants Treated with Systemin Peptide Show Enhanced Levels of Direct and Indirect Defense Associated with Increased Expression of Defense-Related Genes".</p>
In vivo transcriptome of Lactobacillus acidophilus and colonization impact on murine host intestinal gene expression
<p><i>Lactobacillus acidophilus </i>NCFM is a probiotic strain commonly used in dairy products and dietary supplements. Post-genome <i>in vitro </i>studies of NCFM thus far have linked potential key genotypes to its probiotic-relevant attributes including gut survival, prebiotic utilization, host interactions and immunomodulatory activities. To corroborate and extend beyond previous <i>in vivo and</i> <i>in vitro </i>functional studies, we employed a dual RNA-seq transcriptomic approach to identify genes potentially driving the gut fitness and activities of <i>L. acidophilus </i>NCFM<i> in vivo</i>, and in parallel, examine the ileal transcriptional response of its murine hosts during monocolonization. Spatial expression profiling of NCFM from the ileum through the colon revealed a set of 134 core genes that were consistently overexpressed during gut transit. These <i>in vivo </i>core genes are predominantly involved in the metabolism of carbohydrates, amino acids and nucleotides, along with mucus-binding proteins and adhesion factors, confirming their functionally important roles in nutrient acquisition and gut retention. Functional characterization of the highly expressed major S-layer encoding gene established its indispensable role as a cell shape determinant and maintenance of cell surface integrity, essential for viability and probiotic attributes. Host colonization by <i>L. acidophilus</i> resulted in significant down-regulation of several pro-inflammatory cytokines and tight junction proteins. Genes related to redox signaling, mucin glycosylation and circadian rhythm modulation were induced, suggesting impacts on intestinal development and immune functions. Metagenomic analysis of NCFM populations post-colonization demonstrated the genomic stability of <i>L. acidophilus </i>as a gut transient and further established its safety as a probiotic and biotherapeutic delivery platform.</p>
Supplementary Data for "Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia"
<p>These files contain the computational analysis of sequencing data and mass spectrometry data for "Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia" by Takao, Forbes, Uni, and Kentsis et al.</p>
Interaction of field realistic doses of clothianidin and Varroa destructor parasitism on adult honey bee (Apis mellifera L.) health and neural gene expression, and antagonistic effects on differentially expressed genes
<p>While many studies have examined the effects of neonicotinoid insecticides and the parasitic mite <em>Varroa destructor</em> on honey bees (<em>Apis mellifera</em>), more information on the combined effects of such stressors on gene expression, including neural related genes, and their impact on biological pathways is needed. This study analyzed the effects of field realistic concentrations of the neonicotinoid clothianidin on adult bees infested and not infested with <em>V</em>. <em>destructor</em> over 21 consecutive days and then determined bee survivorship, weight, deformed wing virus (DWV) levels and gene expression. <em>V</em>. <em>destructor</em> parasitism with or without clothianidin exposure was significantly associated with decreased survivorship, weight loss and higher DWV levels, while clothianidin exposure was only associated with higher levels of DWV. Expression analysis of the neural genes <em>AmNlg-1</em>, <em>BlCh</em> and <em>AmAChE-2</em> showed that <em>V</em>. <em>destructor</em> caused a significant down-regulation of all of them, whereas clothianidin caused a significant down-regulation of only <em>AmNrx-1</em> and <em>BlCh</em>. An interaction was only detected for <em>AmNrx-1</em> expression. RNAseq analysis showed that clothianidin exposure resulted in 6.5 times more up-regulated differentially expressed genes (DEGs) than <em>V</em>. <em>destructor</em> alone and 123 times more than clothianidin combined with <em>V</em>. <em>destructor</em>. Similar results were obtained with down-regulated DEGs, except for a higher number of DEGs shared between <em>V</em>. <em>destructor</em> and the combined stressors. KEGG (Kyoto Encyclopedia of Genes and Genomes) biological pathway analysis of the DEGs showed that the stressor linked to the highest number of KEGG pathways was clothianidin, followed by <em>V</em>. <em>destructor</em>, and then considerably fewer number of KEGG pathways with the combined stressors. The reduced numbers of DEGs and KEGG pathways associated with the DEGs for the combined stressors compared to the stressors alone indicates that the interaction of the stressors is not additive or synergistic, but antagonistic. The possible implications of the antagonistic effect on the number of DEGs are discussed.</p>
Towards genetic modification of plant-parasitic nematodes: Delivery of macromolecules to male germlines and expression of exogenous mRNA in second stage juveniles
<p>Plant-parasitic nematodes are a current and future threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics. Forward genetics is largely restricted to studies of natural variation in populations, and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate progress in plant-parasitic nematology, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic "tool kit" in plant-parasitic nematodes. We characterise the gonads of male <em>Heterodera schachtii</em> and Meloidogyne hapla in the context of spermatogenesis. We test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of <em>H. schachtii</em> juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, and, taken together, will expedite the development of genetic modification protocols for sedentary endoparasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.</p>
Supporting Data for: Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)
<p><strong>Background:</strong> Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool- plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six different Oenothera harringtonii tissues from each of three linalool+ and linalool- plants.</p> <p><strong>Results: </strong>Three clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts in Oenothera harringtonii, a single allele of which is found exclusively in linalool+ plants.</p> <p><strong>Conclusions:</strong> By using a naturally occurring polymorphism and comparing different tissues, we were able to identify genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool- plants suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.</p>
Data from: Macroevolutionary persistence of heritable endosymbionts: acquisition, retention, and expression of adaptive phenotypes in Spiroplasma
The phylogenetic incongruence between insects and their facultative maternally transmitted endosymbionts indicates that these infections are generally short-lived evolutionarily. Therefore, long-term persistence of many endosymbionts must depend on their ability to colonize and spread within new host species. At least 17 species of Drosophila are infected with endosymbiotic Spiroplasma that have various phenotypic effects. We transinfected five strains of Spiroplasma from three divergent clades into Drosophila neotestacea to test their capacity to spread in a novel host. A strain that causes male killing in Drosophila melanogaster (its native host) also does so in D. neotestacea, even though these host species diverged 40–60 mya. A strain native to D. neotestacea (designated sNeo) and the two other strains of the poulsonii clade of Spiroplasma confer resistance to wasp parasitism, suggesting that this trait may be ancestral within this clade of Spiroplasma. Conversely, no strain other than sNeo conferred resistance to the sterilizing effects of nematode parasitism, suggesting that nematode resistance is a recently derived condition. The apparent addition of nematode resistance to a Spiroplasma lineage that already confers resistance to wasp parasitism suggests endosymbionts can increase the repertoire of traits conducive to their spread. The capacity of an endosymbiont to undergo maternal transmission and express adaptive phenotypes in novel hosts, without requiring a period of host–symbiont co-evolution, enables the spread of such symbionts immediately after the colonization of a new host. This could be critical for the macroevolutionary persistence of facultative endosymbionts whose sojourn times within individual host species are relatively brief.
Data from: Condition-dependent expression of carotenoid- and melanin-based plumage colour of northern flicker nestlings revealed by manipulation of brood size
Carotenoid-based colouration in feathers is widely accepted to be a reliable signal of the health of an individual, but the condition-dependence of melanin-based plumage ornaments has been highly debated. Using broods that were manipulated in size, we tested whether nutritional stress during rearing affected the carotenoid pigmentation in secondary feathers and the size, shape, and symmetry of melanin spots on breast plumage of northern flicker Colaptes auratus nestlings. Two measures of carotenoid colour (chroma and brightness) of secondary flight feathers did not vary according to brood size treatment, but in a larger dataset from the population, carotenoid chroma was positively associated with nestling mass. Nestlings from experimentally enlarged broods had smaller melanin spots than those from reduced broods, which is some of the first experimental evidence that melanin ornament size in growing nestlings is condition-dependent. However, the shape and symmetry of the melanin breast spots was not associated with nestling mass. Sexual dimorphism was apparent in both types of pigmentation and future studies should investigate whether there are any trade-offs for nestlings between investing in carotenoid colouration and melanisation and whether trade-offs differ between the sexes.
Data from: Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq
The sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA-seq techniques, we have characterized the transcriptome of four different tissue types in A. lixula: the 'somatic' tissues (coelomocytes and digestive tissue) and the 'reproductive' tissues (ovary and testis), from two replicated cDNA libraries for each sample. Additionally, we performed a de novo assembly to build the 'reference' transcriptome, pooling reads of the four tissues, to analyse the differential expression (DE) in pairwise comparisons between tissues. The complete de novo assembly yielded 186 084 transcripts, with a sequence size limit of 100 nt, being 31% of them spliced isoforms. Approximately 21% of the transcripts had blast hits against proteins of metazoans (E < 10−5), being less than 2.2% functionally annotated. Between coelomocytes and digestive, 30 794 transcripts showed DE (~11.8% of them with blast hit), and 19 567 transcripts did so between testis and ovary (~28.5% of them with blast hit). Major GO-term categories upregulated in somatic tissues were those related to muscle contraction and energy generation in digestive, and lipid metabolism associated with immune response in coelomocytes. Between reproductive tissues, the major upregulated GO categories were related to energy generation in testis, and negative regulation of nucleotide metabolism in ovary. We particularly screened for a collection of target genes in each tissue because of their relevance for further studies on evolution and adaptation of echinoids.
Data from: The impact of gene expression variation on robustness and evolvability of a developmental gene regulatory network
Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and may promote the accumulation of cryptic genetic variation affecting early stages. Regulatory interactions during later development are typically more sensitive (linear), allowing variation in expression to affect downstream target genes. Variation in skeletal morphology is associated primarily with expression variation of a few, primarily structural, genes at terminal positions within the network. These results indicate that the position and properties of gene interactions within a network can have important evolutionary consequences independent of their immediate regulatory role.
Data from: Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters
1. Complex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint (Ci) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). 2. Here we propose a set of novel parameters to quantify this constraint by extending the trait-gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, e.g., on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. 3. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun-exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). 4. The relative ease of calculation and dimensionless nature of Ci allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints i) among communities from different regions, ii) on different traits across similar environmental gradients, and iii) for the same trait across different gradient-types.
Data from: DNA methylation predicts immune gene expression in introduced house sparrows (Passer domesticus)
Populations undergoing range expansions are often faced with novel selective pressures, and to cope with such challenges, populations must either adapt quickly or exhibit phenotypic plasticity. This latter option allows for rapid phenotypic adjustments and persistence in novel environments, and thus could be advantageous at range‐edges. Our previous research on house sparrows in Kenya—a site of ongoing range expansion— and a growing literature suggests that invasion success is facilitated by epigenetic regulation of gene expression. Previously, we found (i) differences in the expression of a microbial surveillance gene (i.e. Toll‐like receptor 4—TLR4), and (ii) extensive variation in genome‐wide DNA methylation among house sparrows across Kenya. Here, our goal was to investigate whether these two observations are related, specifically whether DNA methylation within a target sequence upstream of the TLR4 transcription start site is associated with variation in TLR4 expression. We found that DNA methylation in the aforementioned region was quite variable among individuals, and variation at one CpG site predicted differences in TLR4 expression. Moreover, we found genetic variation within the same sequence upstream of the TLR4 exon, but this variation did not predict TLR4 expression. To our knowledge, this is the first study to demonstrate an association between DNA methylation and the expression of an ecologically relevant trait in a range‐expanding vertebrate.
Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity
Light induced shifts in cone frequency and opsin expression occur in many aquatic species. Yet little is known about how quickly animals can alter opsin expression and, thereby, track their visual environments. Similarly, little is known about whether adult animals can alter opsin expression or whether shifts in opsin expression are limited to critical developmental windows. We took adult wild caught bluefin killifish (Lucania goodei) from three different lighting environments (spring, swamp, variable), placed them under two different lighting treatments (clear vs. tea-stained water), and monitored opsin expression over four weeks. We measured opsin expression for five previously described opsins (SWS1, SWS2B, SWS2A, RH2-1, LWS) as well as RH2-2 which we discovered via 454 sequencing. We used two different metrics of opsin expression. We measured expression of each opsin relative to a housekeeping gene and the proportional expression of each opsin relative to the total pool of opsins. Population and lighting environment had large effects on opsin expression which were present at the earliest time points indicating rapid shifts in expression. The two measures of expression produced radically different patterns. Proportional measures indicated large effects of light on the SWS1 expression whereas relative measures indicated no such effect. Instead, light had large effects on the relative expression of SWS2B, RH2-2, RH2-1, and LWS. We suggest that proportional measures of opsin expression are best for making inferences about color vision, but that measures relative to a house keeping gene are better for making conclusions about which opsins are differentially regulated.
Differential Proteomic Expression of Equine Cardiac and Lamellar Tissue During Insulin-Induced Laminitis
<p><span><span>Endocrinopathic laminitis is pathologically similar to the multi-organ dysfunction and peripheral neuropathy found in human patients with metabolic syndrome. Similarly, endocrinopathic laminitis has been shown to partially result from vascular dysfunction. However, despite extensive research, the pathogenesis of this disease is not well elucidated and laminitis remains without an effective treatment. Here, we sought to identify novel proteins and pathways underlying the development of equine endocrinopathic laminitis. Healthy Standardbred horses (n=4/group) were either given an electrolyte infusion, or a 48-hour euglycemic-hyperinsulinemic clamp. Cardiac and lamellar tissues were analyzed by mass spectrometry (FDR=0.05). All hyperinsulinemic horses developed laminitis despite being previously healthy. We identified 538 and 737 unique proteins in the cardiac and lamellar proteomes, respectively. In the lamellar tissue, we identified 14 proteins which were significantly upregulated and 13 proteins which were significantly downregulated in the hyperinsulinemic group as compared to controls. These results were confirmed via real-time reverse-transcriptase PCR. A STRING analysis of protein-protein interactions revealed that these upregulated proteins were primarily involved in coagulation and complement cascades, platelet activity, and ribosomal function, while downregulated proteins were involved in focal adhesions, spliceosomes, and cell-cell matrices. Novel significant differentially expressed proteins associated with hyperinsulinemia-induced laminitis include talin -1, vinculin, cadherin-13, fibrinogen, alpha-2-macroglobulin, and heat shock protein 90. In contrast, no proteins were found to be significantly differentially expressed in the heart of hyperinsulinemic horses compared to controls. Together,</span> <span>these data indicate that while hyperinsulinemia induced, in part, microvascular damage, complement activation, and ribosomal dysfunction in the lamellae, but a similar effect was not seen in the heart. In brief, this proteomic investigation of a unique equine model of hyperinsulinemia identified novel proteins and signaling pathways, which may lead to the discovery of molecular biomarkers and/or therapeutic targets for endocrinopathic laminitis.</span></span></p>
Data from: Repeatable glucocorticoid expression is associated with behavioural syndromes in males but not females in a wild primate
Behavioural syndromes are a well-established phenomenon in human and non-human animal behavioural ecology. However, the mechanisms that lead to correlations among behaviours and individual consistency in their expression at the apparent expense of behavioural plasticity remain unclear. The "state-dependent" hypothesis posits that inter-individual variation in behaviour arises from inter-individual variation in state and that the relative stability of these states within an individual leads to consistency of behaviour. The endocrine stress response, in part mediated by glucocorticoids (GCs), is a proposed behavioural syndrome-associated state as GC levels are linked to an individual's behavioural responses to stressors. In this study, in wild Barbary macaques (Macaca sylvanus), consistent inter-individual differences were observed in both sexes for GC activity (faecal glucocorticoid [fGC] concentrations), but not GC variation (coefficient of variation in fGC concentrations). The expression of the behavioural syndrome "Excitability" (characterized by the frequencies of brief affiliation or aggressive interactions) was related to GC activity in males but not in females; more "excitable" males had lower GC activity. There was no relationship in females between any of the behavioural syndromes and GC activity, nor in either sex with GC variation. The negative relationship between GC activity and Excitability in males provides some support for GC expression as a behavioural syndrome-generating state under the state-dependent framework. The absence of this relationship in females highlights that state-behavioural syndrome associations may not be generalizable within a species and that broader sex differences in state need to be considered for understanding the emergence and maintenance of behavioural syndromes.
Data from: Analyzing negative feedback using a synthetic gene network expressed in the Drosophila melanogaster embryo
Background: A complex network of gene interactions controls gene regulation throughout development and the life of the organisms. Insights can be made into these processes by studying the functional interactions (or "motifs") which make up these networks. Results: We sought to understand the functionality of one of these network motifs, negative feedback, in a multi-cellular system. This was accomplished using a synthetic network expressed in the Drosophila melanogaster embryo using the yeast proteins Gal4 (a transcriptional activator) and Gal80 (an inhibitor of Gal4 activity). This network is able to produce an attenuation or shuttling phenotype depending on the Gal80/Gal4 ratio. This shuttling behavior was validated by expressing Gal3, which inhibits Gal80, to produce a localized increase in free Gal4 and therefore signaling. Mathematical modeling was used to demonstrate the capacity for negative feedback to produce these varying outputs. Conclusions: The capacity of a network motif to exhibit different phenotypes due to minor changes to the network in multi-cellular systems was shown. This work demonstrates the importance of studying network motifs in multi-cellular systems.
Data from: Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation
In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals from Atlantic origin including both wild and farmed individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analyzed loci showed deviations from Mendelian segregation after analysis of five full-sib families including ~92 individuals/family. The markers are used to consolidate the turbot genetic map and, since they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) at 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.
Data from: Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern
Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability. We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.
Data from: Multiple signaling in a variable environment: expression of song and color traits as a function of ambient sound and light
Many animals communicate using more than one signal, and several hypotheses exist to explain the evolution of multiple signals. However, these hypotheses typically assume static selection pressures and previous work has not addressed how spatial and temporal environmental variation can shape variation in signaling systems. In particular, environmental variability, such as ambient lighting or noise, may affect efficacy (e.g. detectability/perception by receivers) of signals. To examine how signal expression varies intraspecifically as a function of habitat characteristics, we evaluated relationships between spatial environmental variation and song and plumage color expression in a tropical songbird, the red-throated ant-tanager (Habia fuscicauda) in Panama. We recorded male ant-tanager song, plucked feathers to measure coloration, and recorded the acoustic and light environments from each male's territory. In addition, we took several morphometric measurements from each male to assess the potential information content of song and plumage color. We found that males with redder and more saturated crowns occurred on darker territories, and males that sang shorter and lower frequency songs occurred on noisier territories. We also found that more colorful males tended to sing longer and lower frequency songs. Finally we found that song and color correlated similarly with male morphology (e.g. tarsus length, body mass). Altogether these results indicate that spatial variation in the environment is related to male coloration and song, and that males might be optimizing color and song expression for their particular territorial environment.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.