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2,420 results for “differential gene expression”
Differentially evolutionary pathways and their interactions in genes expressed in brain of human and macaque
As the key organ that separates human from other non-human primates, brain has continuously evolved to adapt to the changes of environments and climates. Although human shares most genetic, molecular and cellular features with primates like macaque, there are significant differences in the structure and function in brain of human and these species. Thus, exploring the differences between brains of human and non-human primates in the context of evolution will provide insights into the development, function and diseases of human nervous system. Since the genes involved in many aspects of human brain are under common pressures of natural selection, their evolutionary features can be analyzed collectively at pathway-level. In this study, we tried to explore the molecular mechanisms underlying human brain by comparing the evolutionary features of pathways enriched in genes expressed in human brain and macaque brain. We identified 31 differentially evolutionary pathways in the brain of human and macaque, among which included those related to neurological diseases, signaling transduction, immune and metabolism. By analyzing differentially expressed genes in brain regions and development stages between human and macaque, we also found that ten and four pathways with evolutionary differences, respectively. We further performed crosstalk analysis of pathways to obtain an intuitive correlation between the pathways, which is helpful to understand the mechanism of interaction between pathways. Our results shed light on a comprehensive view of the evolutionary pathways of the human nervous system and provide a reference for the study of human brain development.
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>
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: Diving into divergence: differentiation in swimming performances, physiology and gene expression between locally-adapted sympatric cichlid fishes
<p>Sympatric speciation occurs without strict vicariance and is thought to often be driven by ecological specialization of subpopulations that eventually diverge genetically and phenotypically. Distinct morphologies between sympatric populations occupying different niches have been interpreted as such differentiating adaptive phenotypes, yet differences in performance and thus adaptiveness between them were rarely tested. Here, we investigated if divergent body shapes of two sympatric crater lake cichlid species from Nicaragua, one being a shore-associated (benthic) species while the other prefers the open water zones (limnetic), affect cruising and sprinting swimming abilities - performances particularly relevant to their respective lifestyles. Furthermore, we investigated species differences in oxygen consumption across different swimming speeds and compare gene expression in gills and white muscle at rest and during exercise. We found a superior cruising ability in the limnetic <i>Amphilophus zaliosus</i> compared to the benthic <i>A. astorquii</i>, while sprinting was not different, suggesting that their distinct morphologies affect swimming performance. Increased cruising <a>ability in <i>A. zaliosus</i> was however linked</a> to a higher oxygen demand, during activity (but not rest), indicating different metabolic rates during exercise - a hypothesis supported by coinciding gene expression patterns of gill transcriptomes. We identified differentially expressed genes linked to swimming physiology, regulation of swimming behaviour and oxygen intake. A combination of physiological and morphological differences may thus underlie adaptations to these species' distinct niches. This complex ecological specialization likely resulted in morphological and physiological trade-offs that contributed to the rapid establishment and maintenance of divergence with gene flow.</p>
Data from: Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus
Anthozoans are a class of Cnidarians that includes scleractinian corals, anemones and their relatives. Despite a global rise in disease epizootics impacting scleractinian corals, little is known about the immune response of this key group of invertebrates. To better characterize the anthozoan immune response, we used the model anemone Exaiptasia pallida to explore the genetic links between the anthozoan-algal symbioses and immunity in a two-factor RNA-Seq experiment using both symbiotic and aposymbiotic(menthol-bleached) Exaiptasia pallida exposed to the bacterial pathogen Vibrio coralliilyticus. Multivariate and univariate analyses of Exaiptasia gene expression demonstrated that exposure to live Vibrio coralliilyticus had strong and significant impacts on transcriptome-wide gene expression for both symbiotic and aposymbiotic anemones, but we did not observe strong interactions between symbiotic state and Vibrio exposure. There were 4,164 significantly differentially expressed (DE) genes for Vibrio exposure, 1,114 DE genes for aposymbiosis, and 472 DE genes for the additive combinations of Vibrio and aposymbiosis. KEGG enrichment analyses identified 11 pathways - involved in immunity (5), transport and catabolism (4) and cell growth and death (2) - that were enriched due to both Vibrio and/or aposymbiosis. Immune pathways showing strongest differential expression included complement, coagulation, nucleotide-binding and oligomerization domain (NOD), and Toll for Vibrio exposure and coagulation and apoptosis for aposymbiosis.
Data from: Differential gene expression in Acromyrmex leaf-cutting ants after challenges with two fungal pathogens
Social insects in general and leaf-cutting ants in particular have increased selection pressures on their innate immune system due to their social lifestyle and monoclonality of the symbiotic fungal cultivar. As this symbiosis is obligate for both parties, prophylactic behavioural defences against infections are expected to increase either ant survival or fungus-garden survival, but also to possibly trade off when specific infections differ in potential danger. We examined the effectiveness of prophylactic behaviours and modulations of innate immune defences by a combination of inoculation bioassays and genome-wide transcriptomic studies (RNA-Seq), using an ant pathogen (Metarhizium brunneum) and a fungus-garden pathogen (Escovopsis weberi) and administering inoculations both directly and indirectly (via the symbiotic partner). Upon detection of pathogen conidia, ant workers responded by increasing both general activity and the frequency of specific defence behaviours (self-grooming, allo-grooming, garden-grooming) independent of the pathogen encountered. This trend was also evident in the patterns of gene expression change. Both direct and indirect (via fungus garden) inoculations with Metarhizium induced a general up-regulation of gene expression, including a number of well-known immune-related genes. In contrast, direct inoculation of the fungus garden by Escovopsis induced an overall down-regulation of ant gene expression, whereas indirect inoculation (via the ants) did not, suggesting that increased activity of ants to remove this fungus-garden pathogen is costly and involves trade-offs with the activation of other physiological pathways.
Data from: De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues
Background: The American lobster, Homarus americanus, is an important species as an economically valuable fishery, a key member in marine ecosystems, and a well-studied model for central pattern generation, the neural networks that control rhythmic motor patterns. Despite multi-faceted scientific interest in this species, currently our genetic resources for the lobster are limited. In this study, we de novo assemble a transcriptome for Homarus americanus using central nervous system (CNS), muscle, and hybrid neurosecretory tissues and compare gene expression across these tissue types. In particular, we focus our analysis on genes relevant to central pattern generation and the identity of the neurons in a neural network, which is defined by combinations of genes distinguishing the neuronal behavior and phenotype, including ion channels, neurotransmitters, neuromodulators, receptors, transcription factors, and other gene products. Results: Using samples from the central nervous system (brain, abdominal ganglia), abdominal muscle, and heart (cardiac ganglia, pericardial organs, muscle), we used RNA-Seq to characterize gene expression patterns across tissues types. We also compared control tissues with those challenged with the neuropeptide proctolin in vivo. Our transcriptome generated 34,813 transcripts with known protein annotations. Of these, 5,000-10,000 of annotated transcripts were significantly differentially expressed (DE) across tissue types. We found 421 transcripts for ion channels and identified receptors and/or proteins for over 20 different neurotransmitters and neuromodulators. Results indicated tissue-specific expression of select neuromodulator (allostatin, myomodulin, octopamine, nitric oxide) and neurotransmitter (glutamate, acetylcholine) pathways. We also identify differential expression of ion channel families, including kainite family glutamate receptors, inward-rectifying K+ (IRK) channels, and transient receptor potential (TRP) A family channels, across central pattern generating tissues. Conclusions: Our transcriptome-wide profiles of the rhythmic pattern generating abdominal and cardiac nervous systems in Homarus americanus reveal candidates for neuronal features that drive the production of motor output in these systems.
Data from: Differential hippocampal gene expression is associated with climate-related natural variation in memory and the hippocampus in food-caching chickadees
There is significant and often heritable variation in cognition and its underlying neural mechanisms, yet specific genetic contributions to such variation are not well characterized. Black-capped chickadees present a good model to investigate the genetic basis of cognition because they exhibit tremendous climate-related variation in memory, hippocampal morphology and neurogenesis rates throughout the North American continent, and these cognitive traits appear to have a heritable basis. We examined the hippocampal transcriptome profiles of laboratory-reared chickadees from the two most divergent populations to test whether differential gene expression in the hippocampus is associated with population differences in spatial memory, hippocampal morphology and adult hippocampal neurogenesis rates. Using high-resolution mRNA sequencing coupled to a de novo transcriptome assembly, we generated 23 295 consensus sequences, which predicted 16 206 protein sequences with 13 982 showing high similarity to known protein sequences or conserved hypothetical proteins in other species. Of these, we identified differential expression in nearly 380 genes, with 47 genes specifically linked to neurogenesis, apoptosis, synaptic function, and learning and memory processes. Many of the other differentially expressed genes, however, may be associated with other functions. Our study presents the first avian hippocampal transcriptome, and it is the first study identifying differential gene expression associated with natural variation in cognition and the hippocampus. Our results provide additional support to the hypothesis that population differences in memory, hippocampal morphology and neurogenesis in chickadees have likely resulted from natural selection that appears to act on memory and its underlying neural mechanisms.
Genetic variability among and within domestic Old and New World Camels at the α-lactalbumin gene (LALBA) reveals new alleles and polymorphisms responsible for differential expression
<p><strong>Supplementary Figure 1</strong>. Schematic representation of the <em>LALBA</em> gene in camelids. Boxes indicate the exons (black for the un-translated, white for the signal peptide and grey for the translated). The line shows introns, 5’- and 3’-flanking regions.</p> <p><strong>Supplementary Figure 2</strong><strong>. </strong>Alignment of the α-LA calcium-binding site (red rectangle) of 23 terrestrial species available in the UniProt database (<a href="http://www.uniprot.org/uniprot/">http://www.uniprot.org/uniprot/</a>). The calcium-binding site in the <em>Camelus dromedarius</em> is indicated by a yellow rectangle.</p>
time course gene expression of atrial cardiomyocyte differentiation
<p>atrial cardiomyocyte protocol was similar to that described by Cyganek et al. 2018</p>
Differential gene expression table of the transcriptional response of Colorado potato beetle to aegerolysin-based complex
<p>The file in Excel format (xlsx) contains the results of differential gene expression analysis of a study with Colorado potato beetle larvae that explores the potential adaptive response of CPB larvae to feeding with feed complemented by the aegerolysin-based complex PlyA2/PlyB.</p> <p>Experimental design: Leptinotarsa decemlineata larvae fed on potato leaf disks supplemented with PlyA2/PlyB/buffer solution vs control larvae fed on leaves soaked in buffer. Whole larvae were sampled at 1 and 5 days post-treatment, and RNA was isolated and sequenced on an Illumina sequencing platform.</p>
Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera
<p><em>Juniperus flaccida</em> (drooping juniper) and <em>Pinus cembroides</em> (pinyon pine) are conifers native to North America, spanning Mexico and the Southwestern region of the United States. Although from two different lineages, both species exhibit heteroblastic growth. Morphologically, their leaves undergo a change between the juvenile and adult life stage. <em>J. flaccida</em> leaves appear needle-like at youth and scale-like at maturity, whereas the <em>P. cembroides</em> will transition from needle-like leaves to brown scale-like leaves. The objective was to perform a comparative transcriptomic analysis to quantify and examine differential expression in juvenile and adult individuals from both species. RNA from twelve samples was sequenced on HiSeq 1500 (100bp PE) and analyzed with available software. Because there are no reference genomes for these species, they were assembled<em> de novo </em>from the RNA-Seq reads. Following assembly, the coding regions were identified and redundant transcripts were removed. Quality filtered reads were aligned to the reference transcriptomes (one for each species), counts were generated from the alignment files, and differential expression analysis was performed with DESeq2 via Kallisto. Up and down-regulated genes (padj<0.1) across both age classes (juvenile vs adult) were observed in each species and compared.</p>
Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed Eimeria species
<p>Coccidiosis caused by the <em>Eimeria</em> species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of <em>Eimeria</em>-infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi). Based on the changes in gene expression patterns, we defined three groups of genes that showed differential expression. This enabled us to capture evidence of endoplasmic reticulum stress at the initial stage of <em>Eimeria</em> infection. Furthermore, we found that innate immune responses against the parasite were activated at the first exposure; they then showed gradual normalization. Although the cytokine-cytokine receptor interaction pathway was significantly operative at 4 dpi, its downregulation led to an anti-inflammatory effect. Additionally, the construction of gene co-expression networks enabled identification of immunoregulation hub genes and critical pattern recognition receptors after <em>Eimeria</em> infection. Our results provide a detailed understanding of the host-pathogen interaction between chicken and <em>Eimeria</em>. The clusters of genes defined in this study can be utilized to improve chickens for coccidiosis control.</p>
S1_The_differentially_expressed_genes_enriched_in_GO_clusters
<p>This is supporting information to the article <em>Downregulation of ammonium uptake improves the growth and tolerance of Kluyveromyces marxianus at high temperature</em>, which has been submitted to <em>MicrobiologyOpen</em>.</p>
Data for: Differentially expressed genes comparing WT plants vs xal1-2
<p><span>The balance between cell proliferation, differentiation, and elongation rates emerge from regulatory gene differentiation networks coupled to various signal transduction pathways, including those of reactive oxygen species (ROS). The <em>Arabidopsis thaliana</em> primary root has become a useful system to unravel such networks, as well as their interaction with signals that alter organ growth. The role of transcription factors, that regulate organ development, in mediating the role of ROS in root growth is just beginning to be studied. Here, we report that the MADS-box transcription factor <em>XAANTAL1</em> (<em>XAL1</em>) mediates hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) role in primary root growth and it is involved in the morphogenesis of the columella stem cell differentiation in response to H<sub>2</sub>O<sub>2</sub>. Interestingly, our data suggest that <em>XAL1</em> is a positive regulator of H<sub>2</sub>O<sub>2</sub> concentration in the root meristem via regulating transcript accumulation of several peroxidases. Moreover, we found that <em>XAL1</em> is necessary for the H<sub>2</sub>O<sub>2</sub>-induced inhibition of primary root growth through the negative regulation activities of the peroxidases and catalases. Furthermore, <em>XAL1</em> and <em>RETINOBLASTOMA-RELATED</em> (<em>RBR</em>) are also necessary to positively regulate columella stem cell differentiation that is triggered by moderate H<sub>2</sub>O<sub>2</sub> treatments. </span></p>
List of differential expressed genes for the different conditions
Open the record for dataset details and reuse information.
Genes with differential expression across ancestries are enriched in ancestry-specific disease effects likely due to gene-by-environment interactions
<p>This repository contains raw data, preprocessing scripts, and analysis code to replicate S-LDXR analysis from Wang et al.</p> <p>The project directory is organized as follows:<br>- `compute_de.r`: The script to compute anc-de genes<br>- `create_annot.100kb.sh`: code to create annotations for S-LDXR<br>- `create_annot.r`: R function used to create annotations for S-LDXR<br>- `DEstats.tgz`: Differential gene expression statistics between EAS and EUR for each 7 main cell types + PCs of each cell within each cell type<br>- `list_genes.txt`: Gene list as QCed as in Gazal et al. 2022 Nat Genet<br>- `Lupus_study_adjusted_compressed.h5ad.gz`: The single-cell dataset of Perez*, Gordon*, Subramaniam* et al. 2022 Science used in this study<br>- `README.sh`: This README file<br>- `sldxr_annotations.tgz`: Main S-LDXR annotations used in this study<br>- `sldxr_ref_files.tgz`: S-LDXR reference files (baseline-LD-X annotations, regression weights and EAS and EUR 1000G genotype reference files)<br>- `sumstats.tgz`: GWAS summary statistics of 31 traits in EAS and EUR populations<br>- `code_figures.tgz`: Code files for main figures</p>
Raw data and metadata associated with the manuscript: "Organ and ontogeny-specific steroidal glycoside diversity is associated with differential expression of steroidal glycoside pathway genes in two Solanum dulcamara leaf chemotypes"
<p>Raw LC-MS and RT-qPCR data and metadata associated with the manuscript: "Ontogeny and organ-specific steroidal glycoside diversity is associated with differential expression of steroidal glycoside pathway genes in two <em>Solanum dulcamara</em> leaf chemotypes", accepted at Plant Biology.</p>
Differential gene expression results from DESeq2
<p>Differential gene expression results from DESeq2</p>
Differential Gene Expression Dataset of Thalassiosira hyalina and Nitzschia frigida: Response to light stress under contemporary and elevated pCO2
<p>This is a time-course gene expression dataset on the transcriptomic responses of <em>Thalassiosira hyalina</em> and <em>Nitzschia frigida</em> to light stress under contemporary and elevated pCO2. The corresponding Sequencing data is deposited at the EBI ArrayExpress database under accession number E-MTAB-6999. Contigs were created with Trinity Assembler and are available under DOI:10.5281/zenodo.3361258</p> <p>The according publication is currently in review (8/6/2019): Higher sensitivity towards light stress and ocean acidification in an Arctic sympagic compared to a pelagic diatom;</p> <p>Author team: Ane C. Kvernvik, Sebastian D. Rokitta, Eva Leu, Lars Harms, Tove M. Gabrielsen, Björn Rost and Clara J. M. Hoppe</p> <p>Do not hesitate to contact the authors if you like more information!</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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