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54,099 results for “Expression”
Data from: Arsenic induces members of the mmu-miR-466-669 cluster which reduces NeuroD1 expression
Chronic arsenic exposure can result in adverse development effects including decreased intellectual function, reduced birth weight, and altered locomotor activity. Previous in vitro studies have shown that arsenic inhibits stem cell differentiation. MicroRNAs (miRNAs) are small non-coding RNAs that regulate multiple cellular processes including embryonic development and cell differentiation. The purpose of this study was to examine whether altered miRNA expression was a mechanism by which arsenic inhibited cellular differentiation. The pluripotent P19 mouse embryonal carcinoma cells were exposed to 0 or 0.5 μM sodium arsenite for 9 days during cell differentiation, and changes in miRNA expression was analyzed using microarrays. We found that the expression of several miRNAs important in cellular differentiation, such as miR-9 and miR-199 were decreased by 1.9- and 1.6-fold respectively following arsenic exposure, while miR-92a, miR-291a, and miR-709 were increased by 3-, 3.7- and 1.6-fold, respectively. The members of the miR-466-669 cluster and its host gene, Scm-Like with four Mbt domains 2 (Sfmbt2), were significantly induced by arsenic from 1.5- to 4-fold in a time-dependent manner. Multiple miRNA target prediction programs revealed that several neurogenic transcription factors appear to be targets of the cluster. When consensus anti-miRNAs targeting the miR-466-669 cluster were transfected into P19 cells, arsenic-exposed cells were able to more effectively differentiate. The consensus anti-miRNAs appeared to rescue the inhibitory effects of arsenic on cell differentiation due to an increased expression of NeuroD1. Taken together, we conclude that arsenic induces the miR-466-669 cluster, and that this induction acts to inhibit cellular differentiation in part due to a repression of NeuroD1.
Data from: Release from intralocus sexual conflict? Evolved loss of a male sexual trait demasculinises female gene expression
The loss of sexual ornaments is observed across taxa, and pleiotropic effects of such losses provide an opportunity to gain insight into underlying dynamics of sex-biased gene expression and intralocus sexual conflict (IASC). We investigated this in a Hawaiian field cricket, Teleogryllus oceanicus, in which an X-linked genotype (flatwing) feminises males' wings and eliminates their ability to produce sexually selected songs. We profiled adult gene expression across somatic and reproductive tissues of both sexes. Despite the feminising effect of flatwing on male wings, we found no evidence of feminised gene expression in males. Instead, female transcriptomes were more strongly affected by flatwing than males', and exhibited demasculinised gene expression. These findings are consistent with a relaxation of IASC constraining female gene expression through loss of a male sexual ornament. In a follow-up experiment we found reduced testes mass in flatwing males, whereas female carriers showed no reduction in egg production. In contrast, female carriers exhibited greater measures of body condition. Our results suggest sex-limited phenotypic expression offers only partial resolution to intralocus sexual conflict, owing to pleiotropic effects of the loci involved. Benefits conferred by release from intralocus conflict could help explain widespread loss of sexual ornaments across taxa.
Data from: Disruption of gene expression in hybrids of the fire ants Solenopsis invicta and Solenopsis richteri
Transcriptome analysis is a powerful tool for unveiling the distribution and magnitude of genetic incompatibilities between hybridizing taxa. The nature of such incompatibilities is closely associated with the evolutionary histories of the parental species and may differ across tissues and between the sexes. In eusocial insects, the presence of castes that experience divergent selection regimes may result in additional distinct patterns of caste-specific hybrid incompatibilities. We analyzed levels of expression of >14,000 genes in two life stages of each caste and sex in the fire ants S. invicta and S. richteri and in their hybrids. We found strong contributions of both developmental stage and caste to gene expression patterns. Hybrid incompatibilities were surprisingly modest: only 32 genes were mis-expressed, indicating low levels of disruption in gene regulation in hybrids. The castes differed in numbers of mis-expressed genes, with males and workers each mis-expressing at least seven times as many genes as queens. Interestingly, homologues of many of the mis-expressed genes have been implicated in behavioral variation in Drosophila melanogaster. General expression profiles of hybrids were more similar to those of S. richteri than S. invicta, presumably because S. richteri trans-regulatory elements tend to be dominant to those of S. invicta and/or because there is an overall bias in the genetic composition of the hybrids towards S. richteri. Altogether, our results suggest that selection acting on each caste may contribute differently to interspecific divergence and speciation in this group of ants.
Data from: Limits to future adaptation in the invasive plant Polygonum cespitosum: expression of functional and fitness traits at elevated CO2
For organisms to adapt to future environments, they must both evolve appropriate functional responses and phenotypically express those responses under future climatic and CO2 conditions. We examined these 2 components of future adaptation in an invasive annual plant (Polygonum cespitosum) by performing a "resurrection" experiment under field conditions simulating a future environment. Resurrection experiments reveal recent evolution by comparing genotypes from natural populations sampled across a multigeneration interval. We collected genotypes from the same 3 North American populations in 1994 and 2005 and raised inbred lines from these collections under free air CO2 enrichment to examine functional and fitness traits expressed in hot, dry conditions at both ambient and elevated CO2 (N = 295 plants). The species has rapidly evolved in its introduced range to increase photosynthetic rate (collection year effect P ≤ 0.011) and delay senescence (P = 0.017) under full-sun, dry field conditions, but these adaptive changes were not expressed when the field environment included elevated CO2 (within-treatment year effect P ≥ 0.20 for both traits). Populations showed different levels of reproductive output and its genetic variance in these novel, stressful conditions. These findings illustrate constraints on evolutionary adaptation to predicted future conditions at both the species and population levels.
Data from: Species-specific plant–soil feedbacks alter herbivore-induced gene expression and defense chemistry in Plantago lanceolata
Plants actively interact with antagonists and beneficial organisms occurring in the above- and belowground domains of terrestrial ecosystems. In the past decade, studies have focused on the role of plant–soil feedbacks (PSF) in a broad range of ecological processes. However, PSF and its legacy effects on plant defense traits, such as induction of defense-related genes and production of defensive secondary metabolites, have not received much attention. Here, we study soil legacy effects created by twelve common grassland plant species on the induction of four defense-related genes, involved in jasmonic acid signaling, related to chewing herbivore defense (LOX2, PPO7), and in salicylic acid signaling, related to pathogen defense (PR1 and PR2) in Plantago lanceolata in response to aboveground herbivory by Mamestra brassicae. We also assessed soil legacy and herbivory effects on the production of terpenoid defense compounds (the iridoid glycosides aucubin and catalpol) in P. lanceolata. Our results show that both soil legacy and herbivory influence phenotypes of P. lanceolata in terms of induction of Pl PPO7 and Pl LOX2, whereas the expression of Pl PR1 and Pl PR2-1 is not affected by soil legacies, nor by herbivory. We also find species-specific soil legacy effects on the production of aucubin. Moreover, P. lanceolata accumulates more catalpol when they are grown in soils conditioned by grass species. Our study highlights that PSF can influence aboveground plant–insect interactions through the impacts on plant defense traits and suggests that aboveground plant defense responses can be determined, at least partly, by plant-specific legacy effects induced by belowground organisms.
Data from: Blood-brain barrier deterioration and hippocampal gene expression in polymicrobial sepsis: an evaluation of endothelial MyD88 and the vagus nerve
Systemic infection can initiate or exacerbate central nervous system (CNS) pathology, even in the absence of overt invasion of bacteria into the CNS. Recent epidemiological studies have demonstrated that human survivors of sepsis have an increased risk of long-term neurocognitive decline. There is thus a need for improved understanding of the physiological mechanisms whereby acute sepsis affects the CNS. In particular, MyD88-dependent activation of brain microvascular endothelial cells and a resulting loss of blood-brain barrier integrity have been proposed to play an important role in the effects of systemic inflammation on the CNS. Signaling through the vagus nerve has also been considered to be an important component of CNS responses to systemic infection. Here, we demonstrate that blood-brain barrier permeabilization and hippocampal transcriptional responses during polymicrobial sepsis occur even in the absence of MyD88-dependent signaling in cerebrovascular endothelial cells. We further demonstrate that these transcriptional responses can occur without vagus nerve input. These results suggest that redundant signals mediate CNS responses in sepsis. Either endothelial or vagus nerve activation may be individually sufficient to transmit systemic inflammation to the central nervous system. Transcriptional activation in the forebrain in sepsis may be mediated by MyD88-independent endothelial mechanisms or by non-vagal neuronal pathways.
Data from: Adaptive differences in circadian clock gene expression patterns and photoperiodic diapause induction in Nasonia vitripennis
Day length (photoperiod) and temperature oscillate daily and seasonally and are important cues for season-dependent behaviour. Larval diapause of the parasitoid Nasonia vitripennis is maternally induced following a certain number of days (switch point) of a given critical photoperiod (CPP). Both the switch point and CPP follow a latitudinal cline in European N. vitripennis populations,. We previously showed that allelic frequencies of the clock gene period correlate with this diapause induction cline. Here, we report that circadian expression of four clock genes, period (per), cryptochrome-2 (cry-2), clock (clk) and cycle (cyc), oscillates as a function of photoperiod and latitude of origin in wasps from populations from the extremes of the cline. Expression amplitudes are lower in northern wasps, indicating a weaker, more plastic, clock. Northern wasps also have a later onset of activity and longer free running rhythms in constant conditions. Per RNAi caused speeding up of the circadian clock, changed the expression of other clock genes and delayed diapause in both southern and northern wasps. These results point towards adaptive latitudinal clock-gene expression differences and to a key role of per in the timing of photoperiodic diapause induction of N. vitripennis.
Data from: The influence of a working memory task on affective perception of facial expressions
In a dual-task paradigm, participants performed a spatial location working memory task and a forced two-choice perceptual decision task (neutral vs. fearful) with gradually morphed emotional faces (neutral ~ fearful). Task-irrelevant word distractors (negative, neutral, and control) were experimentally manipulated during spatial working memory encoding. We hypothesized that, if affective perception is influenced by concurrent cognitive load using a working memory task, task-irrelevant emotional distractors would bias subsequent perceptual decision-making on ambiguous facial expression. We found that when either neutral or negative emotional words were presented as task-irrelevant working-memory distractors, participants more frequently reported fearful face perception - but only at the higher emotional intensity levels of morphed faces. Also, the affective perception bias due to negative emotional distractors correlated with a decrease in working memory performance. Taken together, our findings suggest that concurrent working memory load by task-irrelevant distractors has an impact on affective perception of facial expressions.
Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.
Data from: Effects of cell-cycle-dependent expression on random fluctuations in protein levels
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We analyse a model where a stable protein is synthesized in random bursts, and the frequency with which bursts occur varies within the cell cycle. Formulae quantifying the extent of fluctuations in the protein copy number are derived and decomposed into components arising from the cell cycle and stochastic processes. The latter stochastic component represents contributions from bursty expression and errors incurred during partitioning of molecules between daughter cells. These formulae reveal an interesting trade-off: cell-cycle dependencies that amplify the noise contribution from bursty expression also attenuate the contribution from partitioning errors. We investigate the existence of optimum strategies for coupling expression to the cell cycle that minimize the stochastic component. Intriguingly, results show that a zero production rate throughout the cell cycle, with expression only occurring just before cell division, minimizes noise from bursty expression for a fixed mean protein level. By contrast, the optimal strategy in the case of partitioning errors is to make the protein just after cell division. We provide examples of regulatory proteins that are expressed only towards the end of the cell cycle, and argue that such strategies enhance robustness of cell-cycle decisions to the intrinsic stochasticity of gene expression.
Synchronized reagent delivery in double emulsions for triggering chemical reactions and gene expression
<p>Data underlying the figures in the publication “Synchronized reagent delivery in double emulsions for triggering chemical reactions and gene expression”, published in Small Methods.</p> <p>Table of contents:</p> <p>1. Figure 2C; Origin file containing all data and analysis for Figure 2C. Requires Origin Software to open.</p> <p>2. Figure 3; FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure 3B and 3C. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>200721 FDG in PVA after prod_FDG sample 6_006.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 4 PVA shake_002.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 4 PVA shake_002.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>3. Figure 4BC; Origin file containing all data and analysis for Figure 4B and 4C. Requires Origin Software to open.</p> <p>4. Figure 5; Origin file containing all data and analysis for Figure 5D. Requires Origin Software to open.</p> <p>File Figure 5_201215-new LUVs 500 mM DH5alpha: FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure 5B. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 18h after prod_012.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 3 18h after prod- 05%SDS_018.fcs</p> <p>5. Figure S2; PDF files, report from DLS instrument.</p> <p>6. Figure S4; Excel file containing the values extracted from microscopy images for Figure S4.</p> <p>7. Figure S5; FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure S5. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>200721 FDG in PVA after prod_FDG sample 6_006.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 5 SDS 01 shake_008.fcs</p> <p>200721 FDG in PVA&SDS 4 h after prod_FDG sample 6 SDS 0001 shake_006.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 4 SDS 001 shake_004.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 5 SDS 01 shake_008.fcs</p> <p>200721 FDG in PVA&SDS 22 h after prod_FDG sample 6 SDS 0001 shake_006.fcs</p> <p>8. Figure S6; Origin file containing all data and analysis for Figure S6 left-Requires Origin Software to open-, and Excel file containing the values from 96 well plate measurements used for Figure S6 right.</p> <p>9. Figure S7; Excel files containing the values from 96 well plate measurements used for Figure S7 left, and the values extracted from microscopy images for Figure S7 right.</p> <p>10. Figure S9; FlowJo Workspace for data analysis and fcs raw data acquired from flow cytometer for Figure S9. Requires FlowJo software to open.</p> <p>Raw data file names:</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 3h30min after prod_005.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 18h after prod_012.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 1 30min after prod_001.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 3 3h30min after prod - 05%SDS_008.fcs</p> <p>201215-new LUVs 500 mM-DH5alpha_sample 3 18h after prod- 05%SDS_018.fcs</p>
Data from: Fighting experience alters brain androgen receptor expression dependent on testosterone status
Contest decisions are influenced by the outcomes of recent fights (winner–loser effects). Steroid hormones and serotonin are closely associated with aggression and therefore probably also play important roles in mediating winner–loser effects. In mangrove rivulus fish, Kryptolebias marmoratus, individuals with higher testosterone (T), 11-ketotestosterone and cortisol levels are more capable of winning, but titres of these hormones do not directly mediate winner–loser effects. In this study, we investigated the effects of winning/losing experiences on brain expression levels of the receptor genes for androgen (AR), oestrogen α/β (ERα/β), glucocorticoid (GR) and serotonin (5-HT1AR). The effect of contest experience on AR gene expression depended on T levels: repeated losses decreased, whereas repeated wins increased AR gene expression in individuals with low T but not in individuals with medium or high T levels. These results lend strong support for AR being involved in mediating winner–loser effects, which, in previous studies, were more detectable in individuals with lower T. Furthermore, the expression levels of ERα/β, 5-HT1AR and GR genes were higher in individuals that initiated contests against larger opponents than in those that did not. Overall, contest experience, underlying endocrine state and hormone and serotonin receptor expression patterns interacted to modulate contest decisions jointly.
Data from: Predation risk determines pigmentation phenotype in nuthatches by melanin-related gene expression effects
Pigments determine the appearance of organisms. However, pigment production can be associated to physiological constraints as in the case of pheomelanin, the sulphurated form of melanin whose synthesis in melanocytes consumes cysteine and consequently reduces the availability of glutathione (GSH) to exert antioxidant protection. Pheomelanogenesis may thus increase the susceptibility to suffer chronic oxidative stress. I investigated the possibility that environmental lability in the expression of genes regulating pheomelanogenesis protects from oxidative stress, a situation in which GSH is most required. By broadcasting adult alarm calls, I manipulated the perception of predation risk, a natural source of oxidative stress, in free-living Eurasian nuthatch Sitta europaea nestlings developing pheomelanin-pigmented flank feathers. The manipulation affected the consumption of GSH that resulted from the expression of two genes (Slc7a11 and Slc45a2) influencing cysteine/GSH availability in cells, as these genes were downregulated in the feather melanocytes of the nestlings with lowest intracellular antioxidant capacity (i.e., lowest GSH levels). Systemic oxidative damage increased with Slc7a11 expression in feather melanocytes, suggesting that the observed downregulation was physiologically advantageous. The nestlings exposed to an increased perception of predation risk developed flank feathers of reduced color intensity. These results indicate that perceived predation risk can determine the pigmentation phenotype by (probably epigenetic) effects on gene expression that protect from physiological constraints imposed by pheomelanin production.
Data from: Mining of expressed sequence tag libraries of cacao for microsatellite markes using five computational tools
Expressed Sequence Tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, and data on gene expression and regulation and provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences as available in public domain were downloaded and made into contigs. A total of 769 contigs were made using contigs assembly program pharp. Puative information of contigs were identified using NCBI and ExPASy tools such as BlastX, tblastn.
Data from: Differential gene expression according to race and host plant in the pea aphid
Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences amongst host races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on numerous plants in the Fabaceae and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host plant, indicating the importance of gene expression in aphid–plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host races may result from genetic drift and reproductive isolation and possibly divergent selection. Expression differences related to plant adaptation include a subset of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies' findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change.
Data from: Analysis of expressed sequence tags from the placenta of the live-bearing fish Poeciliopsis (Poeciliidae)
Matrotrophic fish in the genus Poeciliopsis (Poeciliidae) have a placenta-like structure used in post-fertilization maternal provisioning of the developing embryo. To understand better the structure and function of the Poeciliopsis placenta we derived cDNA libraries from the maternal follicular placenta of two matrotrophic Poeciliopsis sister species, P. turneri and P. presidionis. These species inherited their placenta from a common ancestor and represent one of three independent origins of placentas in Poeciliopsis. Expressed sequence tags were generated and putative function was determined using BLASTX homology searches and Gene Ontology annotation. Reverse transcriptase-PCR was used to verify placenta tissue expression of a putative candidate gene, alpha-2 macroglobulin. 1956 (71.5% of the total submitted ESTs) and 924 (71.0% of the total submitted ESTs) unique transcripts were identified for the P. turneri and P. presidionis placenta, respectively. Homology search and Gene Ontology annotation revealed putative genes whose products may be involved in specific transport functions of the maternal follicle. These putative genes are excellent candidates for future research on the evolution of the placenta. We discuss our results in light of the parent-offspring conflict theory of placental evolution and in terms of the Poeciliid placenta structure and function.
Data from: "Meiotic genes" are constitutively expressed in an asexual amoeba and are not necessarily involved in sexual reproduction
The amoebae (and many other protists) have traditionally been considered as asexual organisms but suspicion has been growing that these organisms are cryptically sexual or are at least related to sexual lineages. This contention is mainly based on genome studies in which the presence of "meiotic genes" has been discovered. Using RNA-seq (next generation shotgun sequencing, identifying and quantifying the RNA species in a sample), we have found that the entire repertoire of meiotic genes is expressed in exponentially growing Acanthamoeba and we argue that these so called meiotic genes are involved in the related process of homologous recombination in this amoeba. We contend that they are only involved in meiosis in other organisms that indulge in sexual reproduction and that homologous recombination is important in asexual protists as a guard against the accumulation of mutations. We also suggest that asexual reproduction is the ancestral state.
Data from: Expression of eukaryotic-like protein in the microbiome of sponges
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host-microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood. Here we use metatranscriptomics to investigate ELP expression in the microbiomes of three different sponges (Cymbastella concentrica, Scopalina sp. and Tedania anhelens). We developed a workflow with optimized rRNA removal and in silico subtraction of host sequences to obtain a reliable symbiont metatranscriptome. This showed that between 1.3 and 2.3% of all symbiont transcripts contain genes for ELPs. Two classes of ELPs (cadherin and tetratricopetide repeats) were abundantly expressed by in the C. concentrica and Scopalina sp. microbiomes, while ankyrin repeat ELPs were predominant in the T. anhelens metatranscriptome. Comparison to non-ELP containing transcripts indicated a constitutive expression of ELPs across a range of bacterial and archaeal symbionts. Expressed ELPs also contained domains involved in protein secretion and/or were co-expressed with proteins involved in extra-cellular transport. This suggests these ELPs are likely exported, which could allow for direct interaction with the sponge. Our study shows that ELP genes in sponge symbionts represent actively expressed functions that could mediate molecular interaction between symbiosis partners.
Data from: Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)
Sex chromosomes have evolved independently in phylogenetically diverse flowering plant lineages. The genes governing sex determination in dioecious species remain unknown, but theory predicts that the linkage of genes influencing male and female function will spur the origin and early evolution of sex chromosomes. For example, in an XY system, the origin of an active Y may be spurred by the linkage of female suppressing and male promoting genes. Garden asparagus (Asparagus officinalis) serves as a model for plant sex chromosome evolution, given that it has recently evolved an XX/XY sex chromosome system. In order to elucidate the molecular basis of gender differences and sex determination, we used RNA-sequencing (RNA-Seq) to identify differentially expressed genes between female (XX), male (XY) and supermale (YY) individuals. We identified 570 differentially expressed genes, and showed that significantly more genes exhibited male-biased than female-biased expression in garden asparagus. In the context of anther development, we identified genes involved in pollen microspore and tapetum development that were specifically expressed in males and supermales. Comparative analysis of genes in the Arabidopsis thaliana, Zea mays and Oryza sativa anther development pathways shows that anther sterility in females probably occurs through interruption of tapetum development before microspore meiosis.
Data from: Similarities in temperature-dependent gene expression plasticity across time-scales in threespine stickleback (Gasterosteus aculeatus)
Phenotypic plasticity occurs at a variety of time-scales, but little is known about the degree to which plastic responses at different time-scales are associated with similar underlying molecular processes, which is critical for assessing the effects of plasticity on evolutionary trajectories. To address this issue, we identified differential gene expression in response to developmental temperature in the muscle transcriptome of adult threespine stickleback (Gasterosteus aculeatus) exposed to 12, 18, and 24 °C until hatch and then held at 18 °C for nine months, and compared these results to differential gene expression in response to adult thermal acclimation in stickleback developed at 18 °C and then acclimated to 5 and 25 °C as adults. Adult thermal acclimation affected the expression of 7,940 and 7,015 genes in response to cold and warm acclimation, respectively, and 4,851 of these genes responded in both treatments. In contrast, the expression of only 33 and 29 genes were affected by cold and warm development, respectively. The majority of the genes affected by developmental temperature were also affected by adult acclimation temperature. Many genes that were differentially expressed as a result of adult acclimation were associated with previously identified temperature-dependent effects on DNA methylation patterns, suggesting a role of epigenetic mechanisms in regulating gene expression plasticity during acclimation. Taken together, these results demonstrate similarities between the persistent effects of developmental plasticity on gene expression and the effects of adult thermal acclimation, emphasizing the potential for mechanistic links between plasticity acting at these different life stages.
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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.