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54,099 results for “Expression”
Data from: Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish
Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes. In this study, we utilized RNA-seq to assess transcriptome-wide gene expression in the muscle of Atlantic killifish (Fundulus heteroclitus) from a population that contains segregating variation in mitochondrial genotype. We examined gene expression plasticity in response to 5°C acclimation and the effects of mitochondrial genotype on this plasticity. Cold acclimation resulted in changes in gene expression consistent with up-regulation of genes involved in many cellular functions, including spliceosomal and proteasomal processes, and with down-regulation of genes involved in extracellular matrix, muscle contraction and oxidative phosphorylation functions. There were few differences in gene expression between killifish with different mitochondrial genotypes: 14 genes demonstrated significant interactions between mitochondrial genotype and acclimation temperature and 3 genes demonstrated effects of mitochondrial genotype alone. These results indicate that variation in mitochondrial genotype has modest effects on gene expression; the majority of which are revealed as differences in plasticity as a result of environmental change.
Data from: miR-9a modulates maintenance and ageing of Drosophila germline stem cells by limiting N-cadherin expression
Ageing is characterized by a decline in stem cell functionality leading to dampened tissue regeneration. While the expression of microRNAs across multiple species is markedly altered with age, the mechanism by which they govern stem cell-sustained tissue regeneration is unknown. We report that in the Drosophila testis, the conserved miR-9a is expressed in germline stem cells and its levels are significantly elevated during ageing. Transcriptome and functional analyses show that miR-9a directly regulates the expression of the adhesion molecule N-cadherin (N-cad). miR-9a null mutants maintain a higher number of stem cells even in the aged tissue. Remarkably, this rise fails to improve tissue regeneration and results in reduced male fertility. Similarly, overexpression of N-cad also results in elevated stem cell number and decreased regeneration. We propose that miR-9a downregulates N-cad to enable adequate detachment of stem cells toward differentiation, thus providing the necessary directionality toward terminal differentiation and spermatogenesis.
Data from: Reproductive workers show queen-like gene expression in an intermediately eusocial insect, the buff-tailed bumble bee Bombus terrestris
Bumble bees represent a taxon with an intermediate level of eusociality within Hymenoptera. The clear division of reproduction between a single founding queen and the largely sterile workers is characteristic for highly eusocial species, whereas the morphological similarity between the bumble bee queen and the workers is typical for more primitively eusocial hymenopterans. Also, unlike other highly eusocial hymenopterans, division of labour among worker subcastes is plastic and not predetermined by morphology or age. We conducted a differential expression analysis based on RNA-seq data from 11 combinations of developmental stage and caste to investigate how a single genome can produce the distinct castes of queens, workers and males in the buff-tailed bumble bee Bombus terrestris. Based on expression patterns, we found males to be the most distinct of all adult castes (2411 transcripts differentially expressed compared to nonreproductive workers). However, only relatively few transcripts were differentially expressed between males and workers during development (larvae: 71 and pupae: 162). This indicates the need for more distinct expression patterns to control behaviour and physiology in adults compared to those required to create different morphologies. Among female castes, reproductive workers and their nonreproductive sisters displayed differential expression in over ten times more transcripts compared to the differential expression found between reproductive workers and their mother queen. This suggests a strong shift towards a more queenlike behaviour and physiology when a worker becomes fertile. This contrasts with eusocial species where reproductive workers are more similar to nonreproductive workers than the queen.
Evolution of sex-specific heat stress tolerance and larval Hsp70 expression in populations of Drosophila melanogaster adapted to larval crowding
<p class="BodyA">The ability to tolerate temperature stress is an important component of adult fitness. In holometabolous insects like <i>Drosophila melanogaster,</i> adult stress resistance can be affected by growth conditions experienced during the larval stages. While evolution under crowded larval conditions is known to lead to the correlated evolution of many adult traits, its consequences on adult heat stress tolerance have not been investigated. Therefore, in the present study, we assessed the adult heat stress tolerance in populations of <i>D.</i><i> </i><i>melanogaster</i> adapted to a stressful larval crowding environment. We used replicate populations of <i>D.</i><i> </i><i>melanogaster</i>, selected for adaptation to larval crowding stress (MCUs), for more than 230 generations, and their respective controls (MBs). Larvae from selected and control populations were grown under crowded and uncrowded conditions and their adult heat shock resistance at two different temperatures was measured. Further, we compared Hsp70 expression in crowded and uncrowded larvae of both populations and also measured the Hsp70 expression after a mild-heat treatment in adults of selected and control populations. Our results showed that adaptation to larval crowding leads to the evolution of Hsp70 gene expression in larval stages and improves adult heat-stress tolerance ability in males, but not in females. </p>
Data from: The expression of established cognitive brain states stabilizes with working memory development
We present results from a longitudinal study conducted over 10 years in a sample of 126 8-33 year olds demonstrating that adolescent development of working memory is supported by decreased variability in the amplitude of expression of whole brain states of task-related activity. fMRI analyses reveal that putative gain signals affecting maintenance and retrieval aspects of working memory processing stabilize during adolescence, while those affecting sensorimotor processes do not. We show that trial-to-trial variability in the reaction time and accuracy of eye-movements during a memory guided saccade task are related to fluctuations in the amplitude of expression of task-related brain states, or brain state variability, and also provide evidence that individual developmental trajectories of reaction time variability are related to individual trajectories of brain state variability. These observations demonstrate that underlying the maturation of cognition through adolescence is the stabilization of widespread gain signals affecting already available cognitive processes.
Data from: Genotype-by-environment interactions for cuticular hydrocarbon expression in Drosophila simulans
Genotype-by-environment interactions (G x Es) describe genetic variation for phenotypic plasticity. Recent interest in the role of these interactions in sexual selection has identified G x Es across a diverse range of species and sexual traits. Additionally, theoretical work predicts that G x Es in sexual traits could help to maintain genetic variation, but could also disrupt the reliability of these traits as signals of mate quality. However, empirical tests of these theoretical predictions are scarce. We reared iso-female lines of Drosophila simulans across two axes of environmental variation (diet and temperature) in a fully factorial design and tested for G x Es in the expression of cuticular hydrocarbons (CHCs), a multivariate sexual trait in this species. We find sex-specific environmental, genetic and G x E effects on CHC expression, with G x Es for diet in both male and female CHC profile and a G x E for temperature in females. We also find some evidence for ecological crossover in these G x Es, and by quantifying variance components, genetic correlations and heritabilities, we show the potential for these G x Es to help maintain genetic variation and cause sexual signal unreliability in D. simulans CHC profiles.
ARBic: an all-round biclustering algorithm for analyzing gene expression data
<p>datasets of ARBic: an all-round biclustering algorithm for analyzing gene expression data</p>
Significant differentially expressed genes (DEG) for midgut tissue from bees maintained for four hours at 35°C or 45°C
<p><span><span>Honey bee colonies in the United States have suffered from increased die-off in the last few years with a complex set of interacting stresses playing a key role. With changing climate, an increase in the frequency of severe weather events, such as heat waves, is anticipated. Understanding how these changes may contribute to stress in honey bees is crucial. Individual honey bees appear to have a high capacity to endure thermal stress. One reason for this high-level endurance is likely their robust HSR which contributes to thermotolerance at the cellular level. However, less is known about other mechanisms of thermotolerance, especially those operating at the tissue level. To elucidate other determinants of this resilience in this species, we used <span>thermal stress coupled with RNAseq and identified broad transcriptional remodeling of a number of key signaling pathways in the honey bee, including those pathways known to be involved in digestive tract regeneration in the fruit fly such as the Hippo and JAK/STAT pathways. We also observe cell death and shedding of epithelial cells, which likely leads to induction of this regenerative transcriptional program. </span>We found that thermal stress affects many of these pathways in other tissues, suggesting a shared program of damage response. This study provides important foundational characterization of the tissue damage response program in this key pollinating species. In addition, our data suggest that a robust regeneration program may also be a critical contributor to thermotolerance at the tissue level, a possibility which warrants further exploration in this and other species. </span></span></p>
Figure 1 in No rest for the weary: restricted resting behaviour of green turtles (Chelonia mydas) at a deep-neritic foraging area influences expression of life history traits
Figure 1. Generalised profiles for the six dive types as defined by Seminoff et al. (2006).
A new look at the role of complement circulating in peripheral blood and expressed in hematopoietic stem cells in the regulation of hematopoiesis
<p>Hematopoietic transplantation is performed by intravenous infusion of donor-derived or autologous hematopoietic stem progenitor cells (HSPCs), which, in response to bone marrow (BM)-expressed chemoattractant navigate and home to BM hematopoietic niches. This process is followed by their engraftment and expansion to repopulate the recipient’s BM myeloablated before transplantation. The most important BM chemoattractant is the alpha-chemokine stromal-derived factor 1 (SDF-1). However, its homing role is supported by the bioactive phosphospingolipid sphingosine-1-phosphate (S1P) and by extracellular adenosine triphosphate (eATP). As we demonstrated in the past, the CXCR4 receptor for SDF-1 must be incorporated into cell surface membrane lipid rafts (MLRs) for optimal SDF-1 gradient sensing by HSPCs. Our previous research demonstrated that an important and for many years underestimated role in hematopoiesis plays an innate immunity soluble arm that is complement cascade (ComC). We provided an evidence that ComC becomes activated in BM during pharmacological mobilization in response to granulocyte colony-stimulating factor (G-CSF) or CXCR4 receptor antagonist AMD3100. In this proposal, we will focus on the role of ComC in a reverse phenomenon that is posttransplant homing/engraftment of HSPCs. It is known that the critical step before infusion of HSPCs is the myeloablative treatment of the recipient aimed to destroy pathological hematopoiesis and empty BM niches to provide space available for new transplanted HSPCs. Myeloablative treatment involves high-dose chemotherapy or myeloablative irradiation. In experimental animal transplant models, lethal irradiation is a standard procedure. The available literature indicates that both irradiation and chemotherapy induce in various organs and tissues similarly as during mobilization a state of sterile inflammation and extracellular ATP (eATP) released from damaged cells triggers this process. We postulate that the same occurs in the BM microenvironment, and in fact, our preliminary data shows that ComC becomes activated in mice after myeloablative conditioning for transplantation by lethal gamma-irradiation or exposure to myeloablative chemotherapy. It is known that ComC could be activated by i) classical-, ii) mannan-binding lectin, or iii) alternative-pathway. Activation of ComC leads to the release C3 and C5 complement components cleavage fragments - C3a and C5a anaphylatoxins that are processed by serum carboxypeptidase to desArgC3a and desArgC5a as well as leads to the formation of C5b-C9 or non-lytic or lytic membrane attack complex (MAC), which is the terminal product of ComC activation. On the other hand, both HSPCs and cells in the BM microenvironment express receptors for C3a and C5a (C3aR, C5aR1, and C5aR2). After myeloablative therapy, active ComC cleavage fragments circulate in PB. Therefore, HSPCs infused into the transplant recipient's bloodstream are exposed to these potent innate immunity mediators. This interaction of HSPCs with ComC meditators, as we propose, promotes better navigation of infused cells to the recipient BM niches and we hypothesize is a result of the promotion of MLRs formation on HSPCs. On the other hand, myeloablative conditioning for transplantation induces a state of sterile inflammation in transplant recipient BM to facilitate homing and engraftment of circulating in PB transplanted HSPCs. Finally, new intriguing evidence accumulated that in addition to the liver ComC synthesis occurs also inside some cells – e.g., in lymphocytes. Our recent data indicate that the same phenomenon occurs in HSPCs. Therefore, the intercellular expression of ComC elements known as complosome sheds new light on the underappreciated role of innate immunity in regulating hematopoiesis.</p> <p> </p> <p>This work was supported by the National Science Centre, Poland OPUS grant UMO-2022/45/B/NZ6/00475. </p> <p> </p> <p>The data included in the database were used in the following publications:</p> <p>1. <a href="https://www.nature.com/articles/s41375-024-02188-9" target="_blank" rel="noopener">https://www.nature.com/articles/s41375-024-02188-9</a></p> <p>2. <a href="https://link.springer.com/article/10.1007/s11302-023-09943-0" target="_blank" rel="noopener">https://link.springer.com/article/10.1007/s11302-023-09943-0</a></p> <p>3. <a href="https://www.nature.com/articles/s41375-023-01894-0" target="_blank" rel="noopener">https://www.nature.com/articles/s41375-023-01894-0</a></p>
Large scale expression and purification of full-length huntingtin Q54 with HAP40 from baculoviral expression system production in sf9 insect cells – 2018/08/04
<p><strong>Project</strong> - Huntingtin structure-function open lab notebook. </p> <p><strong>Rationale </strong>- Purified huntingtin samples with and without stabilising binding partners (HAP40) are required for use in structural and functional studies, in particular SAXS experiments. </p>
Gene expression of neurotransmitter receptors over reproductive cycle of Nicrophorus vespilloides
<p>Understanding genetic influences of traits in non-model organisms is crucial to understanding how novel traits arise. Do new traits require new genes, or are old genes repurposed? How predictable is this process? Here we examine this question for gene expression influencing parenting behavior in a beetle, <i>Nicrophorus</i> <i>vespilloides</i>. Parental care, produced from many individual behaviors, should be influenced by changes of expression of multiple genes and one suggestion is that the genes can be predicted based on knowledge of behavior expected to be precursors to parental care, such as, aggression, resource defense, and mating on a resource. Thus, testing gene expression during parental care allows us to test expectations of this "precursor hypothesis" for multiple genes and traits. We tested for changes of the expression of serotonin, octopamine/tyramine, and dopamine receptors, as well as, one glutamate receptor, predicting that these gene families would be differentially expressed during social interactions with offspring and associated resource defense. We found that serotonin receptors were strongly associated with social and aggression behavioral transitions. Octopamine receptors produced a complex picture of gene expression over a reproductive cycle. Dopamine was not associated with the behavioral transitions sampled here, while the glutamate receptor was most consistent with a behavioral change of resource defense/aggression. Our results generate new hypotheses, refine candidate lists for further studies, and inform the genetic mechanisms that are co-opted during the evolution of parent-offspring interactions, a likely evolutionary path for many lineages that become fully social. The precursor hypothesis, while not perfect, does provide a starting point for identifying candidate genes.</p>
Supplementary material 1 from: Rahmadi M, Ardianto C, Nurhan AD, Chasanah RA, Krismonika DI, Puspitasari AD, Suprapti B, Segaran S, Phan C-W, Khotib J (2022) Bisacodyl overcomes morphine-induced constipation by decreasing colonic Aquaporin-3 and Aquaporin-4 expression. Research Results in Pharmacology 8(4): 65-75. https://doi.org/10.3897/rrpharmacology.8.82242
The representative photos of feces with high water content and low water content
Expression of oat metallothioneins in drought-stressed oat seedlings
<p>This .xls file contains results of expression analyses in oat plants. The plants were subjected to drought stress. Shoots and roots of said wlants were collected and ground in liquid nitrogen. RNA was isolated and cDNA was synthesized. the cDNA was used as a template in qPCR analysis. Primers in qPCR were specific for oat metallothionein genes. EIF and HNR genes were used as a reference gene. </p>
Pocillopora and Cladocopium gene expression levels and Cladocopium SNPs
<p><strong>Pocillopora holobiont gene expression levels</strong></p> <p>The following files contain the genes expression levels of <em>Pocillopora </em>and its<em> Cladocopium </em>photosymbiont for102 <em>Pocillopora </em>coral colonies collected in the framework of Tara Pacific expedition.</p> <p>Pocillopora_MetaT_ReadCount.tab : <em>Pocillopora </em>raw read counts</p> <p>Pocillopora_MetaT_TPM.tab : <em>Pocillopora </em>normalized read counts</p> <p>CladocopiumC1_MetaT_ReadCount.tab : <em>Cladocopium </em>raw read counts</p> <p>CladocopiumC1_MetaT_TPM.tab : <em>Cladocopium </em>normalized read counts</p> <p>Methods: Pocillopora fragments from 102 colonies were processed to extract then sequence RNA. Metatranscriptomic reads (Illumina-generated 150-bp, paired-end) were separately aligned to predicted coding sequences (CDS) of the Pocillopora meandrina coral host reference genome, the CDS of the Cladocopium goreaui genome, and a Durusdinium transcriptome using Burrows–Wheeler Transform Aligner (BWA-mem, v0.7.15) with the default settings. Host- and symbiont-mapped reads were then sorted and processed using SAMtools v1.10.282 to generate respective bam files. A read was considered a host contig if its sequence aligned to the P. meandrina predicted coding sequence with ≥ 95% of sequence identity and with ≥ 50% of the sequence aligned. Reads aligned to Cladocopium goreaui coding sequences with a cutoff of ≥ 98% of sequence identity over ≥ 80% of the read length were retained as symbiont reads. Reads were further filtered to remove those in which more than 75% of the read length was low complexity or less than 30% was high complexity. Read counts were normalized as transcript per million (TPM).</p> <p><strong>Cladocopium Variants :</strong></p> <p>The following file contains <em>Cladocopium</em> variants<em> </em>called from metatranscriptomic reads of 82 samples aligned on <em>Cladocopium goreaui </em>coding sequences.</p> <p>Cladocopium_FilteredSNPs_4x.vcf.gz : Filtered variants in each sample in vcf format</p> <p>Cladocopium_FilteredSNPs_4x.freq.tab : Alternative allele frequencies of filtered variants in each sample</p> <p>Method: For Pocillopora colonies hosting Cladocopium (84 colonies) we further investigated their population structure using single nucleotide polymorphism (SNP) distributions across their coding sequences. Briefly, we identified a set of transcriptome-wide single nucleotide polymorphisms (SNPs) from metatranscriptomic reads mapped to the Cladocopium goreaui CDS using the Genome Analysis Toolkit tool (GATK, v3.7.0). We followed a modified version of the best practices guide for variant discovery with GATK which included indexing of the genomic reference (picardtools v2.6.0, CreateSequenceDictionary), followed by identification of realignment targets (GATK RealignerTargetCreator) and realignment around detected indels (GATK, IndelRealigner). Variants were called for each colony individually (GATK, HaplotypeCaller) and resulting variant call files (VCFs) were merged into island-specific, multi-sample, cohort files (GATK, CombineGVCFs) before performing joint genotyping across all 11 islands (GATK, GenotypeGVCFs) with polyploidy defined at 1. Joint analysis of multiple samples (i.e., joint genotyping) is recommended for discovery of germline SNPs and indels as it provides information regarding population-wide variance across a cohort of multiple samples. We excluded from this analysis colonies containing a large proportion (>25%) of a second ITS2 profile and potentially affecting the SNP calling. SNPs were filtered using VCFtools (v0.1.12) to include only biallelic SNPs with a quality score ≥ 30 and a coverage ≥ 4</p>
Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin
<p><span>Naturally occurring point mutations in the <i>HBG</i> promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous<i> HBG1</i> and <i>HBG2 </i>proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions. Among the novel regulatory region identified, base editing at -123 region induced HbF to a higher level than disruption of a well-known BCL11A binding site in erythroblasts derived from healthy donor CD34+ HSPC. We further demonstrated <i>in vitro</i> that the introduction of -123T>C and -124T>C HPFH-like mutations drives gamma-globin expression by creating a <i>de novo</i> binding site for the master erythroid regulator KLF1. Overall, our findings shed light on so far unknown regulatory elements within the <i>HBG</i> promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin. </span></p>
CXCL12 expression predicts survival in Radically Resected (R0) primary pancreatic adenocarcinoma
<p>PDAC CXCR4 CXCL12 CXCR7 PD-L1 dataset</p>
CYP1A expression in freshwater fish of western New York as an indicator of pollution levels
Various species of freshwater fish regulate the expression of certain proteins in response to environmental contamination. Previous research has shown that CYP1A expression increases in response to contaminant levels and can result in increased tumor formation. Fish in contaminated environments would thus benefit by downregulating the expression of CYP1A to reduce tumor prevalence as an adaptive strategy. Alternatively, monitoring of the CYP1A protein in fish can serve as a bioindicator of the pollution level of an environment. This study evaluated CYP1A expression in twelve different species of freshwater fish from seven bodies of water throughout western NY including Cuba Lake, Genesee River, Hanging Bog, Love Canal, Moss Lake, Rushford Lake and Tifft Nature Preserve. Western blot analysis was used to measure CYP1A expression as a marker of site pollution and potential fish population adaptation. It was hypothesized that low CYP1A expression at a site with known contamination would suggest signs of adaptation to pollution levels present. Furthermore, if at least one sample from a species showed CYP1A expression, then the CYP1A antibody (Caymen Chemical, USA; 173132) had compatibility with that species, eliminating falsely suspected adaptation. The results from this study suggest possible adaptation of fish may be occurring in the polluted Tifft Nature Preserve and Genesee River. --
Novel Strategy to Regulate PD-L1 Expression and Enhance Anti-Tumor Effect
<p>Figs source data</p> <p> </p>
Novel Strategy to Regulate PD-L1 Expression and Enhance Anti-Tumor Effect
<p>Figs source dat</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.
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.