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54,099 results for “Expression”
Data from: Gene expression profiling reveals deep-sea coral response to the Deepwater Horizon oil spill
Deep-sea coral communities are key components of the Gulf of Mexico ecosystem and were adversely affected by the Deepwater Horizon (DWH) oil spill. Coral colonies exposed to oil and dispersant exhibited mortality, damage, and physiological signatures of stress. Understanding how corals respond to oil and dispersant exposure at the molecular level is important to elucidate the sub-lethal effects of the DWH disaster, and reveal broader patterns of coral stress responses. Gene expression profiles from RNAseq data were compared between corals at an impacted site and from a reference site. A total of 1,439 differentially expressed genes (≥ 2-fold) were shared among impacted Paramuricea biscaya colonies. Genes involved in oxidative stress, immunity, wound repair, tissue regeneration, and metabolism of xenobiotics were significantly differentially expressed in impacted corals. Enrichment among the over-expressed genes indicates the corals were enduring high metabolic demands associated with cellular stress responses and repair mechanisms. Under-expression of genes vital to toxin processing also suggests a diminished capacity to cope with environmental stressors. Our results provide evidence that deep-sea corals exhibited genome-wide cellular stress responses to oil and dispersant exposure and demonstrate the utility of next-generation sequencing for monitoring anthropogenic impacts in deep waters. These analyses will facilitate the development of diagnostic markers for oil and dispersant exposure in deep-sea invertebrates and inform future oil spill response efforts.
Data from: How symbiosis and ecological context influence the variable expression of transgenerational wing induction upon fungal infection of aphids
Aphids, like most animals, mount a diverse set of defenses against pathogens. For aphids, two of the best studied defenses are symbiont-conferred protection and transgenerational wing induction. Aphids can harbor bacterial symbionts that provide protection against pathogens, parasitoids and predators, as well as against other environmental stressors. In response to signals of danger, aphids also protect not themselves but their offspring by producing more winged than unwinged offspring as a way to ensure that their progeny may be able to escape deteriorating conditions. Such transgenerational wing induction has been studied most commonly as a response to overcrowding of host plants and presence of predators, but recent evidence suggests that pea aphids (Acyrthosiphon pisum) may also begin to produce a greater proportion of winged offspring when infected with fungal pathogens. Here, we explore this phenomenon further by asking how protective symbionts, pathogen dosage and environmental conditions influence this response. Overall, while we find some evidence that protective symbionts can modulate transgenerational wing induction in response to fungal pathogens, we observe that transgenerational wing induction in response to fungal infection is highly variable. That variability cannot be explained entirely by symbiont association, by pathogen load or by environmental stress, leaving the possibility that a complex interplay of genotypic and environmental factors may together influence this trait.
Data from: De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.
Data from: Expressions of nitrate transporter genes reveal different nitrogen statuses of dominant diatom groups in the southern East China Sea
In this study, the mRNA levels of the Nrt2 nitrate transporter gene were used as a molecular indicator of nitrogen status in two dominant diatom groups, Skeletonema and Chaetoceros, which inhabit the southern East China Sea (ECS). To accurately interpret the abundance of Nrt2 transcripts in situ, maximum and minimum expression levels were determined under conditions of nitrogen deprivation and ammonium addition, respectively. In August 2010, Nrt2 transcript levels in Skeletonema at the inner shelf region exhibited a mean of 111 mmole/(mole EFL); at the mid-shelf region, the mean Nrt2 mRNA levels were 298 mmole/(mole EFL), which was very close to the maximum levels observed under nitrogen starvation. By contrast, the Nrt2 transcript levels in Chaetoceros were low at all of the shelf locations, except at one station in the mid-shelf region. The cross-shelf mean was 2.86 mmole/(mole EFL), which was similar to the expression levels observed in cultured Chaetoceros under conditions of sufficient ammonium. Similar expression patterns were observed in diatoms in the southern ECS in June 2011, but the Nrt2 transcript levels in Skeletonema at the inner shelf region were reduced to a mean of 28.6 mmole/(mole EFL). Regression analysis indicated that cell abundance and Nrt2 expression were closely related to the nutricline depth in the coastward half of the southern ECS for Skeletonema but not for Chaetoceros. These results indicate that the evaluated species differ in nitrogen status, which may reflect their evolutionary strategies to survive in a fluctuating marine environment.
Data from: Preadult life history variation determines adult transcriptome expression
Preadult determinants of adult fitness and behavior have been documented in a variety of organisms with complex life cycles, but little is known about expression patterns of genes underlying these adult traits. We explored the effects of differences in egg to adult development time on adult transcriptome and cuticular hydrocarbon variation in order to understand the nature of the genetic correlation between preadult development time and premating isolation between populations of Drosophila mojavensis reared in different host cactus environments. Transcriptome variation was analyzed separately in flies reared on each host and revealed that hundreds of genes in adults were differentially expressed (FDR P < 0.05) due to development time differences. For flies reared on pitaya agria cactus, longer preadult development times caused increased expression of genes in adults enriched for ribosome production, protein metabolism, chromatin remodeling, and regulation of alternate splicing and transcription. Baja California flies reared on organ pipe cactus showed fewer differentially expressed genes in adults due to longer preadult development time, but these were enriched for ATP synthesis and the TCA cycle. Mainland flies reared on organ pipe cactus with shorter development times showed increased transcription of genes enriched for mitochondria and energy production, protein synthesis, and glucose metabolism: adults with longer development times had increased expression of genes enriched for adult life span, cuticle proteins and ion binding, although most differentially expressed genes were unannotated. Differences due to population, sex, mating status, and their interactions were also assessed. Adult cuticular hydrocarbon profiles also showed shifts due to egg to adult development time, and were influenced by population and mating status. These results help to explain why preadult life history variation determines subsequent expression of the adult transcriptome along with traits involved with reproductive isolation and revealed previously undocumented connections between genetic and environmental influences over the entire life cycle in this desert insect.
Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
Data from: Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon.
In vitro experimental evolution has taught us many lessons on the molecular bases of adaptation. To move towards more natural settings, evolution in the mice gut has been successfully performed. Yet, these experiments suffered from the use of laboratory strains as well as the use of axenic or streptomycin treated mice to maintain the inoculated strains. To circumvent these limitations, we conducted a one-year experimental evolution in vivo using a natural isolate of E. coli, strain 536, in conditions mimicking as much as possible natural environment with mother to offspring microbiota transmission. Mice were then distributed in 24 independent cages and separated in two different diets: a regular one (Chow diet, CD) and high-fat high-sugar one (Western diet, WD). Genome sequences revealed an early and rapid selection during the breast-feeding period that selected the constitutive expression of the well-characterized lactose operon. E. coli was lost significantly more in CD than WD, however, we could not detect any genomic signature of selection, nor any diet specificities during the later part of the experiments. The apparently neutral evolution presumably due to low population size maintained nevertheless at high frequency the early selected mutations affecting lactose regulation. The rapid loss of lactose operon regulation challenges the idea that plastic gene expression is both optimal and stable in the wild.
Data from: Reef-specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica)
Understanding the interaction between phenotypic plasticity and evolutionary processes is important for predicting a species' response to changing environment. Strong recurrent selection each generation may be an important process in highly fecund species with broad dispersal and extensive early mortality. We tested whether selection was associated with spatial divergence in gene expression plasticity for osmoregulation in the eastern oyster (Crassostrea virginica). We collected adult oysters from high and low salinity reefs within a single estuary and after 9 weeks of acclimation at 10 and 30 salinity, measured gene expression in 24 oysters using next-generation RNA sequencing technology. The oysters had significantly different expression (DE) in response to salinity treatments for 7936 (18.9%) transcripts overall, with planned contrasts showing 8× more DE in oysters from the high-salinity reef and 15× more DE between reefs when tested at 10 salinity. The reef-by-treatment interaction was also genomically pervasive (5858 DE transcripts, 13.9%). Inter-reef F ST for transcript SNPs averaged 0.0025 with the top 1% between 0.29 and 0.73. Transcripts containing "outlier" SNPs were significantly enriched for osmoregulatory genes and showed patterns of variation consistent with selection on the low-salinity reef. Both phenotypic plasticity and recurrent selection seem to be important factors determining the realized niche of oysters within estuaries.
Targeted genome editing in vivo corrects a Dmd duplication restoring wild‐type dystrophin expression
<p class="Paragraph">Tandem duplication mutations are increasingly found to be the direct cause of many rare heritable diseases, accounting for up to 10% of cases. Unfortunately, animal models recapitulating such mutations are scarce, limiting our ability to study them and develop genome editing-based therapies. Here, we describe the generation of the <em>Dup18-30 </em>mouse model, harbouring a multi-exonic tandem duplication in the <i>Dmd</i> gene which recapitulates a human mutation. Duplication correction of this mouse was achieved by implementing a single-guide RNA (sgRNA) CRISPR/Cas9 approach. This strategy precisely removed a duplication mutation <i>in vivo</i>, restored full-length dystrophin expression, and was accompanied by improvements in both histopathological and clinical phenotypes. We conclude that CRISPR/Cas9 represents a powerful tool to accurately model and treat tandem-duplication mutations. </p> <p class="Paragraph">This dataset includes the deep amplicon sequencing analysis performed to detect single-sgRNA/Cas9 off-target and on-target effects in the <em>Dup18-30</em> mice after treatment.</p>
Videos for MRC5 cells stably expressing GFP-Rab5
<p>Videos of MRC5 cells stably expressing GFP-Rab5.</p>
Pragmatic prediction in the processing of referring expressions containing scalar quantifiers
<p>Data and analysis scripts pertaining to a study by Macuch Silva & Franke (submitted).</p>
Data from: Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize
<p><span><span><span><span><span><span><span><span><span><span><span>Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for prediction within populations. However, it usually cannot capture the complex effects due to combination of alleles in haplotypes. Therefore, accuracy across populations has usually been low. Here we present a novel and cost-effective method for imputing <i>cis</i> haplotype associated RNA expression (HARE, RNA expression of genes by haplotype), studied their transferability across tissues, and evaluated genomic prediction models within and across populations. HARE focuses on tightly linked <i>cis</i> acting causal variants in the immediate vicinity of the gene, while excluding <i>trans</i> effects from diffusion and metabolism, so it would be more transferrable across different tissues and populations. We showed that HARE estimates captured one-third of the variation in gene expression and were more transferable across diverse tissues than the measured transcript expression. HARE estimates were used in genomic prediction models evaluated within and across two diverse maize panels – a diverse association panel (Goodman Association panel) and a large half-sib panel (Nested Association Mapping panel) – for predicting 26 complex traits. HARE resulted in up to 15% higher prediction accuracy than control approaches that preserved haplotype structure, suggesting that HARE carried functional information in addition to information about haplotype structure. The largest increase was observed when the model was trained in the Nested Association Mapping panel and tested in the Goodman Association panel. Additionally, HARE yielded higher within-population prediction accuracy as compared to measured expression values. The accuracy achieved by measured expression was variable across tissues whereas accuracy using HARE was more stable across tissues. Therefore, imputing RNA expression of genes by haplotype is stable, cost-effective, and transferable across populations.</span></span></span></span></span></span></span></span></span></span></span></p>
TWAS weights for expression and splicing in three human spinal cord segments
<p>TWAS weights files from three human spinal cord segments, created with FUSION.</p> <p>Each file consists of a tar.gz compressed directory containing RData files, readable with the R programming language.</p> <p>For expression weights, each RData file is a set of TWAS models for a single gene.</p> <p>For splicing weights, each RData file is a set of TWAS models for a single mRNA splicing junction read, created using Leafcutter.</p>
Supplementary files for manuscript "Effects of deoxynivalenol and fumonisins fed in combination on beef cattle: Immunotoxicity and gene expression "
<p>Supplementary data files for manuscript "Effects of deoxynivalenol and fumonisins fed in combination on beef cattle: Immunotoxicity and gene expression" submitted to the journal <em>Toxins</em>.</p>
Expression Pattern of the Pneumocystis jirovecii Major Surface Glycoprotein Superfamily in Patients with Pneumonia
<p>Data set and description analyses for manuscript Schmid-Siegert et al. 2021 Journal of Infectious diseases.</p>
Figure 4 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 4. Depth versus duration of resting bouts for (a) each individual turtle (n = 12), and (b) average dive depth vs. dive duration for all resting dives by each individual turtle ± 1 standard deviation (R2 = 0.36).
Figure 3 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 3. Dive depth vs. dive duration for (a) all non-resting dives by all turtles (R2 = 0.26, slope = 0.72) and (b) all resting dives by all turtles (R2 = 0.31, slope = 0.43).
Figure 2 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 2. Map of Bahίa de los Angeles study area along the eastern coast of the Baja California Peninsula, Mexico (inset); 10-m baythmetric contours represented by dashed lines; Capture sites: 1. El Barco, 2. La Silica, 3. El Bajo, 4. El Cardon, 5. Pedregal de la Blanca and 6. Playa Blanca.
Fig. 4 in Identification and Expression Patterns of Sensory Neuron Membrane Protein Genes from Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae)
Fig. 4. Relative expression levels of SzeaSNMP in various tissues of Sitophilus zeamais. mAn = male antennae; fAn = female antennae; H = heads without antennae; T = thoraces without legs and wings; Abd = abdomens; W = wings; L = legs. Error bars represent the standard error, and the different letters above each bar indicate significant differences in relative levels of expression at P <0.05 (Tukey's HSD test).
Fig. 2 in Identification and Expression Patterns of Sensory Neuron Membrane Protein Genes from Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae)
Fig. 2. Sequence alignments of Sitophilus zeamais sensory neuron membrane protein with SNMPs from other Coleoptera species. Black triangles represent six conserved cysteine residues that could form three pairs of disulphide bridges in the SNMPs (Rasmussen et al. 1998). Abbreviated species names and GenBank accession numbers of amino acid sequences are described in Fig. 3.
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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.