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54,099 results for “Expression”
Data from: A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells
Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ∼6000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This data set, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).
Data from: Sex-specific gene expression in the mouse nucleus accumbens before and after cocaine exposure
Females are more sensitive than males to the addictive effects of cocaine and are more likely to relapse. The nucleus accumbens has a well-established major role in the response to cocaine, and sex-specific differential expression of key transcripts at baseline and after cocaine withdrawal could underlie some of these differences. To address this hypothesis, four groups of mice (cycling females, ovariectomized females treated with estradiol or placebo and males) were evaluated for open field activity following 7 daily injections of saline or cocaine. Sensitization to the locomotor effects of cocaine was most pronounced in ovariectomized mice receiving estradiol, was greater in cycling females than in males, and failed to occur in ovariectomized/placebo mice. After a 28-day period of withdrawal, RNA prepared from the nucleus accumbens of individual cocaine or saline injected mice was subjected to RNASeq analysis. Expression of a substantial fraction of the transcripts expressed in the nucleus accumbens (~3%) differed in cycling female mice when compared to male mice, was altered by ovariectomy or was responsive to estradiol treatment. The transcripts differentially expressed in the nucleus accumbens of cycling female mice withdrawn from cocaine for 28-days exhibited substantial overlap with those differentially expressed in the nucleus accumbens of male mice withdrawn for 7-days. A small set of transcripts were similarly affected by cocaine in placebo or estradiol treated ovariectomized mice. Transcripts differentially expressed after 28-days of withdrawal encoded neprilysin, which degrades enkephalin and other neuropeptides, G protein coupled receptors and secreted proteins such as Wnt2, Fst and Igfbp4.
Data from: Performance of gene expression analyses using de novo assembled transcripts in polyploid species
Motivation: Quality of gene expression analyses using de novo assembled transcripts in species that experienced recent polyploidization remains unexplored. Results: Differential gene expression (DGE) analyses using putative genes inferred by Trinity, Corset and Grouper performed slightly differently across five plant species that experienced various poly-ploidy histories. In species that lack recent polyploidy events that occurred in the past several millions of years, DGE analyses using de novo assembled transcriptomes identified 54–82% of the differen-tially expressed genes recovered by mapping reads to the reference genes. However, in species that experienced more recent polyploidy events, the percentage decreased to 21–65%. Gene co-expression network analyses using de novo assemblies vs. mapping to the reference genes recov-ered the same module that significantly correlated with treatment in one species that lacks recent polyploidization.
Data from: Gene expression levels are correlated with synonymous codon usage, amino acid composition and gene architecture in the red flour beetle, Tribolium castaneum
Gene expression levels correlate with multiple aspects of gene sequence and gene structure in phylogenetically diverse taxa suggesting an important role of gene expression levels in the evolution of protein-coding genes. Here we present results of a genome-wide study of the influence of gene expression on synonymous codon usage, amino acid composition and gene structure in the red flour beetle, Tribolium castaneum. Consistent with the action of translational selection, we find that synonymous codon usage bias increases with gene expression. However, the correspondence between tRNA gene copy number and optimal codons is weak. At the amino acid level, translational selection is suggested by the positive correlation between tRNA gene numbers and amino acid usage which is stronger for highly expressed genes. In addition, there is a clear trend for increased use of metabolically cheaper, less complex, amino acids as gene expression increases. tRNA gene numbers also correlate negatively with amino acid size/complexity score indicating the coupling between translational selection and selection to minimize the use of large/complex amino acids. Interestingly, the correlation between tRNA gene numbers and amino acid size/complexity score appears to be widespread given our analyses of 10 additional genomes and might be explained by selection against negative consequences of protein misfolding. At the level of gene structure, three major trends are detected 1) CDS length increases across low and intermediate expression levels but decreases in highly expressed genes; 2) the average intron size shows the opposite trend, first decreasing with expression, followed by a slight increase in highly expressed genes and 3) intron density remains nearly constant across all expression levels. These changes in gene architecture are only in partial agreement with selection favoring reduced cost of biosynthesis.
Data from: Gene expression changes in male accessory glands during ageing are accompanied by reproductive decline in Drosophila melanogaster
Senescence is accompanied by loss of reproductive functions. Here we studied reproductive ageing in Drosophila melanogaster males and asked whether the expected decline in male reproductive success is due to diminished functionality of the male accessory gland. The male accessory gland produces the majority of seminal fluid proteins (SFPs) transferred to the female at mating. SFPs induce female post-mating changes and are key to male reproductive success. We measured age-dependent gene expression changes for five representative SFP genes in males from four different age groups ranging from one to six weeks after eclosion. Simultaneously, we also measured male reproductive success in post-mating traits mediated by transfer of these five SFPs. We found a decrease in male SFP gene expression with advancing age and an accompanying decline in male post-mating success. Hence, male reproductive senescence is associated with a decline in functionality of the male accessory gland. While overall individual SFP genes decrease in expression our results point towards the idea that the composition of an ejaculate might change with male age as the rate of change was variable for those five genes.
Data from: Brain size and the expression of pheomelanin-based colour in birds
Eumelanin and pheomelanin are the most common vertebrate pigments. They generate different colours and are synthesized under different physiological conditions. While pheomelanogenesis requires high levels of a key intracellular antioxidant (glutathione, GSH), eumelanogenesis is inhibited by GSH. This implies that species that present the molecular basis to produce large amounts of pheomelanin might be more limited to perform other costly processes that generate oxidative stress than species that produce eumelanin. Brain development requires large amounts of energy and antioxidants during ontogeny, so that large-brained species may be constrained in their simultaneous synthesis of large amounts of pheomelanin, but not in their synthesis of eumelanin. Here we tested this hypothesis in a large dataset of 323 bird species. After controlling for the effects of phylogeny, latitude and sexual dichromatism, the proportion of pheomelanic plumage colour was strongly negatively related to the relative brain mass of species, while no relationship was found for the proportion of eumelanic colour. This indicates that the production of pheomelanin is a costly process that cannot evolve together with complex neural structures and thus with large cognitive capacity. This is the first time that the expression of melanic traits is found to correlate with another phenotypic character across species.
Data from: Estrogen receptor alpha distribution and expression in the social neural network of monogamous and polygynous Peromyscus
In microtine and dwarf hamsters low levels of estrogen receptor alpha (ERa) in the bed nucleus of the stria terminalis (BST) and medial amygdala (MeA) play a critical role in the expression of social monogamy in males, which is characterized by high levels of affiliation and low levels of aggression. In contrast, monogamous Peromyscus males display high levels of aggression and affiliative behavior with high levels of testosterone and aromatase activity. Suggesting the hypothesis that in Peromyscus ERa expression will be positively correlated with high levels of male prosocial behavior and aggression. ERa expression was compared within the social neural network, including the posterior medial BST, MeA posterodorsal, medial preoptic area (MPOA), ventromedial hypothalamus (VMH), and arcuate nucleus in two monogamous species, P. californicus and P. polionotus, and two polygynous species, P. leucopus and P. maniculatus. The results supported the prediction, with male P. polionotus and P. californicus expressing higher levels of ERa in the BST than their polygynous counter parts, and ERa expression was sexually dimorphic in the polygynous species, with females expressing significantly more than males in the BST in both polygynous species and in the MeA in P. leucopus. Peromyscus ERa expression also differed from rats, mice and microtines as in neither the MPOA nor the VMH was ERa sexually dimorphic. The results supported the hypothesis that higher levels of ERa are associated with monogamy in Peromyscus and that differential expression of ERa occurs in the same regions of the brains regardless of whether high or low expression is associated with social monogamy. Also discussed are possible mechanisms regulating this differential relationship.
Data from: Expression and function of ATP-dependent potassium channels in zebrafish islet β-cells
ATP-sensitive potassium channels (KATP channels) are critical nutrient sensors in many mammalian tissues. In the pancreas, KATP channels are essential for coupling glucose metabolism to insulin secretion. While orthologous genes for many components of metabolism–secretion coupling in mammals are present in lower vertebrates, their expression, functionality and ultimate impact on body glucose homeostasis are unclear. In this paper, we demonstrate that zebrafish islet β-cells express functional KATP channels of similar subunit composition, structure and metabolic sensitivity to their mammalian counterparts. We further show that pharmacological activation of native zebrafish KATP using diazoxide, a specific KATP channel opener, is sufficient to disturb glucose tolerance in adult zebrafish. That β-cell KATP channel expression and function are conserved between zebrafish and mammals illustrates the evolutionary conservation of islet metabolic sensing from fish to humans, and lends relevance to the use of zebrafish to model islet glucose sensing and diseases of membrane excitability such as neonatal diabetes.
Can an android's posture and movement discriminate against the ambiguous emotion perceived from its facial expressions?
<p>Android's face and body expressions for experiment stimuli.</p>
Data from: PCR duplication: a one-step cloning-free method to generate duplicated chromosomal loci and interference-free expression reporters in yeast
Here, we report on a novel PCR targeting-based strategy called 'PCR duplication' that enables targeted duplications of genomic regions in the yeast genome using a simple PCR-based approach. To demonstrate its application we first duplicated the promoter of the FAR1 gene in yeast and simultaneously inserted a GFP downstream of it. This created a reporter for promoter activity while leaving the FAR1 gene fully intact. In another experiment, we used PCR duplication to increase the dosage of a gene in a discrete manner, from 1× to 2x. Using TUB4, the gene encoding for the yeast γ-tubulin, we validated that this led to corresponding increases in the levels of mRNA and protein. PCR duplication is an easy one-step procedure that can be adapted in different ways to permit rapid, disturbance-free investigation of various genomic regulatory elements without the need for ex vivo cloning.
Data from: Effects of multi-generational stress exposure and offspring environment on the expression and persistence of transgenerational effects in Arabidopsis thaliana
Plant phenotypes can be affected by environments experienced by their parents. Parental environmental effects are reported for the first offspring generation and some studies showed persisting environmental effects in second and further offspring generations. However, the expression of these transgenerational effects proved context-dependent and their reproducibility can be low. Here we study the context-dependency of transgenerational effects by evaluating parental and transgenerational effects under a range of parental induction and offspring evaluation conditions. We systematically evaluated two factors that can influence the expression of transgenerational effects: single- versus multiple-generation exposure and offspring environment. For this purpose, we exposed a single homozygous Arabidopsis thaliana Col-0 line to salt stress for up to three generations and evaluated offspring performance under control and salt conditions in a climate chamber and in a natural environment. Parental as well as transgenerational effects were observed in almost all traits and all environments and traced back as far as great-grandparental environments. The length of exposure exerted strong effects; multiple-generation exposure often reduced the expression of the parental effect compared to single-generation exposure. Furthermore, the expression of transgenerational effects strongly depended on offspring environment for rosette diameter and flowering time, with opposite effects observed in field and greenhouse evaluation environments. Our results provide important new insights into the occurrence of transgenerational effects and contribute to a better understanding of the context-dependency of these effects.
Data from: Predation risk drives the expression of mobbing across bird species
Many species approach predators to harass and drive them away, even though mobbing a predator can be deadly. However, not all species display this behavior, and those that do can exhibit different behaviors while mobbing different predators. Here we experimentally assessed the role of social and ecological traits on the expression of mobbing behavior in a bird community in SE Brazil (n=157 species). We exposed birds to models of two morphologically similar diurnal owls that pose different risks, and assessed which species engaged in mobbing. Among those that mobbed, we evaluated how they adjusted their mobbing behavior depending on the predator type. We tested the hypothesis that only species that are at risk and can afford to mob engage in this anti-predator behavior. We found that species that engaged in mobbing are in the body mass range of potential prey, forage in the understory or in the canopy, and form flocks. A species' social system did not influence its mobbing behavior. Furthermore, species that engaged in mobbing formed larger mobbing assemblages when facing a high-risk predator, but mobbed more intensely when facing a low-risk predator. Our findings support our predictions, namely that the expression of mobbing is limited by its costs.
Data from: Morphological convergence between an allopolyploid and one of its parental species correlates with biased gene expression and DNA loss
The contribution of gene expression modulation to phenotypic evolution is of major importance to an understanding of the origin of divergent or convergent phenotypes during and following polyploid speciation. Here we analysed genome-wide gene expression in two subspecies of the allotetraploid species, Senecio mohavensis A. Gray, and its diploid parents S. flavus (Decne.) Sch. Bip. and S. glaucus L.. The tetraploid is morphologically much more similar to S. flavus, leading to earlier confusion over its taxonomic status. By means of an analysis of transcriptomes of all three species, we show that gene expression divergence between the parent species is relatively low (ca. 14% of loci), whereas there is significant unequal expression between ca. 20-25% of the parental homoeologues (gene copies) in the tetraploid. The majority of the expression bias in the tetraploid is in favour of S. flavus homoeologues (ca. 65% of the differentially expressed loci), and overall expression of this parental species sub-genome is higher than that of the S. glaucus sub-genome. To determine whether absence of expression of a particular S. glaucus homoeologue in the allotetraploid could be due to loss of DNA, we carried out a PCR-based assay and confirmed that in three out of 10 loci the S. glaucus homoeologue appeared absent. Our results suggest that biased gene expression is one cause of the allotetraploid S. mohavensis being more similar in morphology to one of its parent, S. flavus, and that such bias could result, in part, from loss of S. glaucus homoeologues at some loci in the allotetraploid.
Data from: Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms
Evolutionary Rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23°C to 32°C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations experiencing the slowest rate of temperature increase were the least likely to become extinct and tended to be the best adapted to the new temperature environment. All high-temperature populations were more tolerant to severe heat stress (35°C, 37°C), indicating a common mechanism of heat protection. High-temperature populations also had superior growth rates at optimum temperatures, leading to the absence of a pattern of local adaptation to control (23°C) and high-temperature (32°C) environments. However, high-temperature populations had reduced growth at low temperatures (5-9°C), causing a shift in the temperature niche. In part, the observed evolutionary change can be explained by selection from standing variation. Using mitochondrial markers, we found complete divergence between control and high-temperature populations in the frequencies of six initial founder genotypes. Our results confirm basic predictions of ER and illustrate how adaptation to an extreme local environment can produce positive as well as negative correlated responses to selection over the entire range of the ecological niche.
Data from: Lateralized feeding behavior is associated with asymmetrical neuroanatomy and lateralized gene expressions in the brain in scale-eating cichlid fish
Lateralized behavior ('handedness') is unusual, but consistently found across diverse animal lineages, including humans. It is thought to reflect brain anatomical and/or functional asymmetries, but its neuro-molecular mechanisms remain largely unknown. Lake Tanganyika scale-eating cichlid fish, Perissodus microlepis show pronounced asymmetry in their jaw morphology as well as handedness in feeding behavior – feeding scales preferentially only from one or the other side of their victims. This makes them an ideal model in which to investigate potential laterality in neuroanatomy and transcription in the brain in relation to behavioral handedness. After determining behavioral handedness in P. microlepis (preferred attack side), we estimated the volume of the hemispheres of brain regions and captured their gene expression profiles. Our analyses revealed that the degree of behavioral handedness is mirrored at the level of neuroanatomical asymmetry, particularly in the tectum opticum. Transcriptome analyses showed that different brain regions (tectum opticum, telencephalon, hypothalamus and cerebellum) display distinct expression patterns, potentially reflecting their developmental interrelationships. For numerous genes in each brain region, their extent of expression differences between hemispheres was found to be correlated with the degree of behavioral lateralization. Interestingly, the tectum opticum and telencephalon showed divergent biases on the direction of up- or down-regulation of the laterality candidate genes (e.g., grm2) in the hemispheres, highlighting the connection of handedness with gene expression profiles and the different roles of these brain regions. Hence, handedness in predation behavior may be caused by asymmetric size of brain hemispheres and also by lateralized gene expressions in the brain.
A new mechanism for a familiar mutation – bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement
<p>The <i>DGAT1</i> gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following <i>in-vitro</i> studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. In the current study, we used a large RNAseq dataset to re-examine the underlying mechanisms of this large milk production QTL, and hereby report novel expression-based functions of the chr14 g.1802265AA>GC variant that encodes the <i>DGAT1 </i>K232A substitution. Using expression QTL (eQTL) mapping, we demonstrate a highly-significant mammary eQTL for <i>DGAT1, </i>where the K232A mutation appears as one of the top associated variants for this effect. By conducting <i>in vitro</i> expression and splicing experiments in bovine mammary cell culture, we further show modulation of splicing efficiency by this mutation, likely through disruption of an exon splice enhancer as a consequence of the allele encoding the 232A variant. Although the relative contributions of the enzymatic and transcription-based mechanisms now attributed to K232A remain unclear, these results suggest that transcriptional impacts contribute to the diversity of lactation effects observed at this locus.</p>
Data from: Gene expression stasis and plasticity following migration into a foreign environment
Selection against migrants is key to maintaining genetic differences between populations linked by dispersal. However, migrants may mitigate fitness costs by proactively choosing among available habitats, or by phenotypic plasticity. We previously reported that a reciprocal transplant of lake and stream stickleback (Gasterosteus aculeatus) found little support for divergent selection. Here, we revisit that experiment to test whether phenotypic plasticity in gene expression may have helped migrants adjust to unfamiliar habitats. We measured gene expression profiles in stickleback via TagSeq and tested whether migrants between lake and stream habitats exhibited a plastic response to their new environment that allowed them to converge on the expression profile of adapted natives. We report extensive gene expression differences between genetically divergent lake and stream stickleback, despite gene flow. But for many genes, expression was highly plastic. Fish transplanted into the adjoining habitat partially converged on the expression profile typical of natives from their new habitat. This suggests that expression plasticity may soften the impact of migration. Nonetheless, lake and stream fish differed in survival rates and parasite infection rates in our study, implying that expression plasticity is not fast or extensive enough to fully homogenize fish performance.
Data from: Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms
Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 hours post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to pCO2-acidified seawater to identify genes correlated with initial shell deposition. By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.
Data from: Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across-generations in Daphnia
Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., 'within-generation phenotypic plasticity') as well as induce heritable phenotypic responses that persist for multiple generations (i.e., 'transgenerational plasticity'). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within- and trans-generational plasticity at the molecular level is unclear. Here we tested the influence of fish predator chemical cues on patterns of gene expression within- and across-generations using a clone of Daphnia ambigua that is known to exhibit strong transgenerational plasticity but weak within-generation plasticity. Daphnia were reared in the presence of predator cues in generation 1 and shifts in gene expression were tracked across two additional asexual experimental generations that lacked exposure to predator cues. Initial exposure to predator cues in generation 1 was linked to ~50 responsive genes but such shifts were 3-4x larger in later generations. Differentially expressed genes included those involved in reproduction, exoskeleton structure, and digestion; major shifts in expression of genes encoding ribosomal proteins were also identified. Furthermore, shifts within the first generation and transgenerational shifts in gene expression were largely distinct in terms of the genes that were differentially expressed. Such results argue that the gene expression programs involved in within- versus trans-generation plasticity are fundamentally different. Our study provides new key insights into the plasticity of gene expression and how it relates to phenotypic plasticity in nature.
Data from: Maternal stress has divergent effects on gene expression patterns in the brains of male and female threespine stickleback
Maternal stress can have long-term effects on neurodevelopment that can influence offspring performance and population evolutionary trajectories. To examine the mechanistic basis for these neurodevelopmental effects of maternal stress, we used RNA-seq to assess differential gene expression across the brain transcriptome of adult male and female threespine stickleback (Gasterosteus aculeatus) from stressed and unstressed mothers. We identified sexually divergent effects of maternal stress on the brain transcriptome. In males, genes that were up-regulated by maternal stress were enriched for processes involved in synaptic function and organization and steroid hormone mediated signaling pathways, whereas in females genes that were up-regulated by maternal stress were enriched for processes involved in protein translation and metabolic functions. The expression of several genes involved in the hypothalamic-pituitary-interrenal response to stress and epigenetic processes such as the regulation of DNA methylation patterns and miRNAs increased in males and not in females. These data suggest that maternal stress has markedly different effects on cellular pathways in the brains of male and female offspring of mothers that are exposed to stress, which could have important implications when assessing the long-term ecological and evolutionary impacts of stress across generations.
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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.