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54,099 results for “Expression”
Data from: Gene expression in the phenotypically plastic Arctic charr (Salvelinus alpinus): a focus on growth and ossification at early stages of development
Gene expression during development shapes the phenotypes of individuals. Although embryonic gene expression can have lasting effects on developmental trajectories, few studies consider the role of maternal effects, such as egg size, on gene expression. Using qPCR, we characterize relative expression of 14 growth and/or skeletal promoting genes across embryonic development in Arctic charr (Salvelinus alpinus). We test to what extent their relative expression is correlated with egg size and size at early life‐stages within the study population. We predict smaller individuals to have higher expression of growth and skeletal promoting genes, due to less maternal resources (i.e., yolk) and prioritization of energy toward ossification. We found expression levels to vary across developmental stages and only three genes (Mmp9, Star, and Sgk1) correlated with individual size at a given developmental stage. Contrary to our hypothesis, expression of Mmp9 and Star showed a non‐linear relationship with size (at post fertilization and hatching, respectively), whilst Sgk1 was higher in larger embryos at hatching. Interestingly, these genes are also associated with craniofacial divergence of Arctic charr morphs. Our results indicate that early life‐stage variation in gene expression, concomitant to maternal effects, can influence developmental plasticity and potentially the evolution of resource polymorphism in fishes.
A multidimensional approach to the expression of phenotypic plasticity
<p>Phenotypic plasticity is increasingly recognized as a key element of eco-evolutionary dynamics, but it remains challenging to assess because of its multidimensional nature. Indeed, organisms live in complex environments where numerous factors can impact the phenotypic expression of traits (inter-environment axis), possess multiple traits that can influence each other's expression (inter-trait axis), and differ in their genetic background (inter-genotype axis), which can not only impact the traits' values but also their plasticity.</p> <p>We addressed six questions related to phenotypic plasticity: (1) do different environmental gradients show similar effects on a given trait? (2) Are the effects of two environmental gradients on a trait additive? (3) Do different traits show similar plastic response to a given environmental gradient? (4) Do the (co)variances between traits vary across environmental gradients? (5) Do genotypes differ in their plastic response to a given environmental gradient? (6) Are some genotypes more plastic than others across all traits?</p> <p>We designed a microcosm experiment using the protist Tetrahymena thermophila aimed at encompassing all these aspects of phenotypic plasticity. We exposed 15 distinct genotypes to 25 combinations of temperature and nutrient availability and assessed the plasticity of five phenotypic traits.</p> <p>Our results show strong differences in the plastic response depending on the environmental gradient, not only regarding the shape of the reaction norm of the different traits tested, but also in the overall plasticity of the organisms. We did not find any covariance between traits that was consistent across all environments.</p> <p>Overall, our results suggest independent impacts of the environmental dimension considered on the observed plastic response. These results underline potential difficulties in generalising findings about plasticity to all environments and all traits.</p>
Data from: Testosterone regulates CYP2J19-linked carotenoid signal expression in male red-backed fairywrens (Malurus melanocephalus)
<p>Carotenoid pigments produce most red, orange, and yellow colours in vertebrates. This coloration can serve as an honest signal of quality that mediates social and mating interactions, but our understanding of the underlying mechanisms that control carotenoid signal production, including how different physiological pathways interact to shape and maintain these signals, remains incomplete. We investigated the role of testosterone in mediating gene expression associated with a red plumage sexual signal in red-backed fairywrens (<i>Malurus melanocephalus</i>). In this species, males within a single population can flexibly produce either red/black nuptial plumage or female-like brown plumage. Combining correlational analyses with a field-based testosterone implant experiment and qPCR, we show that testosterone mediates expression of carotenoid-based plumage in part by regulating expression of CYP2J19, a ketolase gene associated with ketocarotenoid metabolism and pigmentation in birds. This is the first time that hormonal regulation of a specific genetic locus has been linked to carotenoid production in a natural context, revealing how endocrine mechanisms produce sexual signals that shape reproductive success.</p>
Differentiation of parathyroid hormone expressing cells from human pluripotent stem cells
Abstract Differentiation of pluripotent stem cells into functional parathyroid-like cells would accelerate development of important therapeutic options for subjects with parathyroid-related disorders, from the design and screening of novel pharmaceutical agents to the development of durable cellular therapies. We have established a highly reproducible directed differentiation approach leading to parathyroid hormone (PTH) expressing cells from human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC). We accomplished this through the comparison of multiple different basal media, the inclusion of the CDK inhibitor PD0332991 in both definitive endoderm (DE) and anterior foregut endoderm (AFE) stages, and a 2-stage pharyngeal endoderm (PE) series. This is the first protocol to reproducibly establish PTH expressing-cells from human pluripotent stem cells and represents a first step towards the development of functional parathyroid cells with broad applicability for medicinal and scientific investigation.
Data from: Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling
In mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and its link to fitness-related behaviors are not well understood. From vomeronasal transcriptomes, we discovered the first evidence of intact vomeronasal type-1 receptor (V1r) genes in bats, and we tested whether putatively functional bat receptors were orthologous to those of related taxa, or whether bats have evolved novel receptors. Instead of lineage-specific duplications, we found that bat V1rs in bats show high levels of orthology to those of their relatives, and receptors are under comparative levels of purifying selection compared to non-bats. Despite widespread vomeronasal organ loss in bats, V1r copies have been retained for >65 million years. The highly conserved nature of bat V1rs challenges our current understanding of mammalian V1r function and suggest roles other than conspecific recognition or mating initiation in social behavior.
RBBP4__1-425_NHis_Expression and Purification Protocol
<p>RBBP4__1-425_NHis_Expression and Purification Protocol</p>
Glucose transporter expression and regulation following a fast in the ruby-throated hummingbird, Archilochus colubris
Hummingbirds, subsisting almost exclusively on nectar sugar, face extreme challenges to blood sugar regulation. The capacity for transmembrane sugar transport is mediated by the activity of facilitative glucose transporters (GLUTs) and their localisation to the plasma membrane (PM). In this study, we determined the relative protein abundance of GLUT1, GLUT2, GLUT3, and GLUT5 via immunoblot using custom antibodies in whole-tissue and PM fractions of flight-muscle, heart, and liver of ruby-throated hummingbirds (Archilochus colubris). GLUTs examined were detected in nearly all tissues tested. Hepatic GLUT1 was minimally present in whole-tissue and absent in PM fractions. GLUT5 was expressed in flight-muscles at levels comparable to that of their liver, consistent with hummingbird flight-muscles' hypothesised uniquely high fructose-uptake and oxidation capacity. To assess GLUT regulation, we fed ruby-throated hummingbirds 1M sucrose ad libitum for 24 hours followed by either 1 hour of fasting or continued feeding until sampling. We measured relative GLUT abundance and concentrations of circulating sugars. Blood fructose concentration in fasted hummingbirds declined (∼5 mM to ∼0.18 mM), while fructose-transporting GLUT2 and GLUT5 abundance did not change in PM fractions. Blood glucose concentrations remained elevated in fed and fasted hummingbirds (∼30 mM), while glucose-transporting GLUT1 and GLUT3 in flight muscle and liver PM fractions, respectively, declined in fasted birds. Our results suggest that glucose uptake capacity is dynamically reduced in response to fasting, allowing for maintenance of elevated blood glucose levels, while fructose uptake capacity remains constitutively elevated promoting depletion of blood total fructose within the first hour of a fast.
Data and code for: Male-male contest limits the expression of assortative mate preferences in a polymorphic poison frog
<p>Co-divergence of sexual traits and mate preferences can lead to assortative mating and subsequently reproductive isolation. However, mate choice rarely operates without intrasexual competition, and the effects of the latter on speciation are often overlooked. Maintaining trait polymorphisms despite gene flow and limiting assortative female preferences for less-competitive male phenotypes are two important roles that male-male competition may play in the speciation process. Both roles rely on the assumption that male-male competition limits the expression of divergent female preferences. We tested this assumption in the highly color-polymorphic strawberry poison frog (<i>Oophaga pumilio</i>). Females prefer males of the local color, suggesting that reproductive isolation may be evolving among color morphs. However, this inference does not account for male-male competition, which is also color-mediated. We housed females with two differently-colored males, and compared reproductive patterns when the more attractive male was the territory holder <i>versus</i> when he was the non-territorial male. Females mated primarily with the territory winner, regardless of coloration, suggesting that when a choice must be made between the two, male territoriality overrides female preferences for male coloration<i>.</i> Our results highlight the importance of considering the combined effects of mate choice and intrasexual competition in shaping phenotypic divergence and speciation.</p>
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.
Protein expression of hepatocellular carcinoma in a fibrotic liver in mice
<p>Hepatocellular carcinoma (HCC) is a liver tumor that arises in patients with cirrhosis. One of the key players in the progression of cirrhosis to HCC is the hepatic stellate cell, which is activated during liver damage. Activated stellate cells play an essential role in the pathogenesis of HCC by creating a fibrotic micro-environment that sustains tumor growth and by producing growth factors and cytokines that enhance tumor cell proliferation and migration. We assessed the role of endoplasmic reticulum (ER) stress in the cross-talk between hepatic stellate cells and HCC-cells. Mice with a fibrotic HCC were treated with the IRE1A-inhibitor 4mu8C. The oncogenic protein expression was assessed using a multiplex proximity extension assay for ninety-two biomarkers in the murine exploratory panel (Olink Bioscience, Uppsala, Sweden) in liver samples from healthy mice, mice with HCC and mice with HCC treated with the IRE1A-inhibitor 4mu8C.</p>
Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera.</p> <p>The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.</p>
Gene expression dynamics during rapid organismal diversification of African cichlid fishes
<p>Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic divergence. Here, we studied gene expression evolution in a model system of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By comparing gene expression profiles of six different organs in 74 cichlid species representing all subclades of this radiation, we demonstrate that the rate of gene expression evolution varies among organs, transcriptome parts, and the subclades of the radiation, indicating different strengths of selection. We found that the non-coding part of the transcriptome evolved more rapidly than the coding part, and that the gonadal transcriptomes evolved more rapidly than the somatic ones, with the exception of liver. We further show that the rate of gene-expression change was not constant over the course of the radiation but accelerated at its later phase. Finally, we show that – at the per-gene level – the evolution of expression patterns is dominated by stabilizing selection.</p>
I see how you feel: facial expressions' recognition and distancing in the time of COVID-19
<p>Data sets and R script for anlysis.</p>
Gene expression and splicing counts from the Kremer et al study
<p><strong>File description:</strong></p> <ol> <li> <p>geneCounts: gene-level counts </p> </li> <li> <p>k_j: split counts spanning from one exon to another.</p> </li> <li> <p>k_theta: non-split counts covering a splice site</p> </li> <li> <p>n_psi3: total split counts from a given acceptor site</p> </li> <li> <p>n_psi5: total split counts from a given donor site</p> </li> <li> <p>n_theta: total split and non-split counts for a given splice site</p> </li> <li> <p>Sample annotation describing each sample from the dataset</p> </li> <li> <p>Description file with global information from the dataset</p> </li> </ol> <p> </p> <p>The gene counts were originated using the GTF file from release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a>, and the split and non-split counts contain only the annonated junctions from the same release.</p> <p><strong>Use: </strong>The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>).</p> <p><strong>Number of samples: </strong>119<br> <strong>Tissue:</strong> Fibroblast<br> <strong>Organism:</strong> Homo sapiens<br> <strong>Genome assembly:</strong> hg19<br> <strong>Gene annotation:</strong> gencode34<br> <strong>Disease (ICD-10: N):</strong> E75: 1, E79: 13, E88: 84, G31: 9, K72: 3, NONE: 9<br> <strong>Strand specific: </strong>FALSE<br> <strong>Paired end: </strong>TRUE<br> <strong>Protocol: </strong>poly(A) enrichment<br> <strong>Dataset contact: </strong>Vicente Yepez, yepez@in.tum.de; Christian Mertes, mertes@in.tum.de; Julien Gagneur, gagneur@in.tum.de; Holger Prokisch, prokisch@helmholtz-muenchen.de</p> <p><strong>Citation:</strong> Cite both the resource using Zenodo's citation and the publication under References</p>
Comparative gene expression analysis reveals mechanism of Pinus contorta response to the fungal pathogen Dothistroma septosporum
<p>Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study,<span> w</span>e investigated the gene expression response of lodgepole pine (<i>Pinus contorta</i>) to attack by the fungal pathogen <i>Dothistroma septosporum</i>, which causes <i>Dothistroma </i>needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two <i>D. septosporum</i> isolates and analyzed the differentially expressed genes, differential exon usage, and co-expressed gene modules using RNA-seq data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one <i>D. septosporum</i> isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene-module-identified genes to the reference plant-pathogen interaction pathway deposited in KEGG database. These genes are present in PAMP-triggered and effector-triggered immunity pathways, including genes encoding mitogen-activated protein kinase and disease resistance protein. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to <i>D. septosporum</i> effectors. Taken together, our results show that gene expression response to <i>D. septosporum</i> infection in lodgepole pine varies both among tree genotypes and pathogen strains, and involves both known candidate genes and a number of genes with previously unknown functions.</p>
DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon
<p>Supplementary Information for the manuscript: "DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon"</p>
Dataset related to article "Optimization of a Luciferase-Expressing Non-Invasive Intrapleural Model of Malignant Mesothelioma in Immunocompetent Mice"
<p>This record contains data related to article "Optimization of a Luciferase-Expressing Non-Invasive Intrapleural Model of Malignant Mesothelioma in Immunocompetent Mice"</p> <p>Malignant Pleural Mesothelioma (MPM) is an aggressive tumor of the pleural lining that is usually identified at advanced stages and resistant to current therapies. Appropriate pre-clinical mouse tumor models are of pivotal importance to study its biology. Usually, tumor cells have been injected intraperitoneally or subcutaneously. Using three available murine mesothelioma cell lines with different histotypes (sarcomatoid, biphasic, epithelioid), we have set up a simplified model of in vivo growth orthotopically by inoculating tumor cells directly in the thorax with a minimally invasive procedure. Mesothelioma tumors grew along the pleura and spread on the superficial areas of the lungs, but no masses were found outside the thoracic cavity. As observed in human MPM, tumors were highly infiltrated by macrophages and T cells. The luciferase-expressing cells can be visualized in vivo by bioluminescent optical imaging to precisely quantify tumor growth over time. Notably, the bioluminescence signal detected in vivo correctly matched the tumor burden quantified with classical histology. In contrast, the subcutaneous or intraperitoneal growth of these mesothelioma cells was considered either non-representative of the human disease or unreliable to precisely quantify tumor load. Our non-invasive in vivo model of mesothelioma is simple and reproducible, and it reliably recapitulates the human disease.</p>
REV-ERBalpha mediates complement expression and circadian regulation of microglial synaptic phagocytosis
<p>The circadian clock has been shown to regulate various aspects of brain health including microglial and astrocyte activation. Here we report that deletion of the master clock protein BMAL1 induces robust increases in the expression of complement genes such as <i>C3, C4b </i>and <i>C1q</i> in the hippocampus. Loss of downstream REV-ERBa-mediated transcriptional repression led to increases in <i>C4b </i>in neurons and astrocytes as well as C3 protein in microglia and astrocytes. REV-ERBa deletion induced complement <i>C3/C4b </i>gene expression and increased microglial phagocytosis of synapses in the CA3 region of the hippocampus. Finally, we observed diurnal variation in the degree of microglial synaptic phagocytosis in wild type mice which was abrogated by REV-ERBα deletion. This work uncovers the BMAL1-REV-ERBa axis as a regulator of complement expression and synaptic phagocytosis in the brain, thereby illuminating a novel mechanism of synaptic regulation by the circadian clock.</p>
The social function of the feeling and expression of guilt
<p>Humans are uniquely cooperative and form crucial short- and long-term social bonds between individuals that ultimately shape human societies. The need for such intense cooperation may have provided a particularly powerful selection pressure on the emotional and communicative behaviours regulating cooperative processes, such as guilt. Guilt is a social, other-oriented moral emotion that promotes relationship repair and pro-sociality. For example, people can be more lenient towards wrongdoers who display guilt than towards those who do not. Here, we examined the social consequences of guilt in a novel experimental setting with pairs of friends differing in relationship quality. Pairs of participants took part in a cooperative game with a mutual goal. We then induced guilt in one of the participants and informed the other participant of their partner's wrongdoing. We examined the outcome using a dictator game to see how they split a joint reward. We found that guilty people were motivated to repair wrongdoing regardless of friendship. Observing guilt in others led to a punishment effect and a victim of wrongdoing punished close friends who appeared guilty more so than acquaintances. We suggest, therefore, that guilt has a stronger function between close friends as the costs of relationship breakdown are greater. Relationship context, therefore, is crucial to the functional relevance of moral emotions.</p>
YAP and TAZ maintain PROX1 expression in the developing lymphatic and lymphovenous valves in response to VEGF-C signaling
<p>Lymphatic vasculature is an integral part of digestive, immune and circulatory systems. The homeobox transcription factor PROX1 is necessary for the development of lymphatic vessels, lymphatic valves (LVs) and lymphovenous valves (LVVs). We and others previously reported a feedback loop between PROX1 and Vascular Endothelial Growth Factor-C (VEGF-C) signaling. PROX1 promotes the expression of the VEGF-C receptor VEGFR3 in lymphatic endothelial cells (LECs). In turn, VEGF-C signaling maintains PROX1 expression in LECs. However, the mechanisms of PROX1/VEGF-C feedback loop remain poorly understood. Whether VEGF-C signaling is necessary for LV and LVV development is also unknown. Here, we report for the first time that VEGF-C signaling is necessary for valve morphogenesis. We have also discovered that the transcriptional co-activators YAP and TAZ are required to maintain PROX1 expression in LVs and LVVs in response to VEGF-C signaling. Deletion of <i>Yap</i> and <i>Taz</i> in the lymphatic vasculature of mouse embryos did not affect the formation of LVs or LVVs, but resulted in the degeneration of these structures. Our results have identified VEGF-C/YAP/TAZ as a critical molecular pathway in valve development.</p>
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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.
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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.