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1,161 results for “Drosophila melanogaster”
Total RNA-seq from Drosophila melanogaster.
GEO Series GSE163852. Drosophila melanogaster. 2 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Effect of RNAi-mediated knockdown of cac on gene expression in motor neurons of Drosophila melanogaster third instar larva
GEO Series GSE301255. Drosophila melanogaster. 9 samples. Type: Expression profiling by high throughput sequencing.
Expression profiling pooled Drosophila melanogaster heterozygous for deletions on Chromosome 2L
GEO Series GSE61509. Drosophila melanogaster. 396 samples. Type: Expression profiling by high throughput sequencing.
Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChIPseq-PolII-S5]
GEO Series GSE116886. Drosophila melanogaster. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Data from: Association between nucleotide variation in Efgr and wing shape in Drosophila melanogaster
As part of an effort to dissect quantitative trait locus effects to the nucleotide level, association was assessed between 238 single-nucleotide and 20 indel polymorphisms spread over 11 kb of the Drosophila melanogaster Egfr locus and nine relative warp measures of wing shape. One SNP in a conserved potential regulatory site for a GAGA factor in the promoter of alternate first exon 2 approaches conservative experimentwise significance (P < 0.00003) in the sample of 207 lines for association with the location of the crossveins in the central region of the wing. Several other sites indicate marginal association with one or more other aspects of shape. No strong effects of sex or population of origin were detected with measures of shape, but two different sites were strongly associated with overall wing size in interaction with these fixed factors. Whole-gene sequencing in very large samples, rather than selective genotyping, would appear to be the only strategy likely to be successful for detecting subtle associations in species with high polymorphism and little haplotype structure. However, these features severely limit the ability of linkage disequilibrium mapping in Drosophila to resolve quantitative effects to single nucleotides.
Data from: The effect of diet and time after bacterial infection on fecundity, resistance, and tolerance in Drosophila melanogaster
Mounting and maintaining an effective immune response in the face of infection can be costly. The outcome of infection depends on two host immune strategies: resistance and tolerance. Resistance limits pathogen load, while tolerance reduces the fitness impact of an infection. While resistance strategies are well studied, tolerance has received less attention, but is now considered to play a vital role in host–pathogen interactions in animals. A major challenge in ecoimmunology is to understand how some hosts maintain their fitness when infected while others succumb to infection, as well as how extrinsic, environmental factors, such as diet, affect defense. We tested whether dietary restriction through yeast (protein) limitation affects resistance, tolerance, and fecundity in Drosophila melanogaster. We predicted that protein restriction would reveal costs of infection. Because infectious diseases are not always lethal, we tested resistance and tolerance using two bacteria with low lethality: Escherichia coli and Lactococcus lactis. We then assayed fecundity and characterized bacterial infection pathology in individual flies at two acute phase time points after infection. As expected, our four fecundity measures all showed a negative effect of a low-protein diet, but contrary to predictions, diet did not affect resistance to either bacteria species. We found evidence for diet-induced and time-dependent variation in host tolerance to E. coli, but not to L. lactis. Furthermore, the two bacteria species exhibited remarkably different infection profiles, and persisted within the flies for at least 7 days postinfection. Our results show that acute phase infections do not necessarily lead to fecundity costs despite high bacterial loads. The influence of intrinsic variables such as genotype are the prevailing factors that have been studied in relation to variation in host tolerance, but here we show that extrinsic factors should also be considered for their role in influencing tolerance strategies.
Data from: The effect of gut microbiota elimination in Drosophila melanogaster: a how-to guide for host-microbiota studies
In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host physiology, ecology, behaviour, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster. We test the efficacy of a low-dose streptomycin diet, egg dechorionation, and an axenic or sterile diet, in the removal of gut bacteria within this species in a fully factorial design. We further determine potential side effects of these methods on host physiology by performing a series of standard physiological assays. Our results showed that individuals from all treatments took significantly longer to develop, and weighed less, compared to normal flies. Males and females that had undergone egg dechorionation weighed significantly less than streptomycin reared individuals. Similarly, axenic female flies, but not males, were much less active when analysed in a locomotion assay. All methods decreased the egg to adult survival, with egg dechorionation inducing significantly higher mortality. We conclude that low-dose streptomycin added to the dietary media is more effective at removing the gut bacteria than egg dechorionation and has somewhat less detrimental effects to host physiology. More importantly, this method is the most practical and reliable for use in behavioural research. Our study raises the important issue that the efficacy of and impacts on the host of these methods, requires investigation in a case by case manner, rather than assuming homogeneity across species and laboratories.
Data from: Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster
Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought.
Data from: Experimental evolution under fluctuating thermal conditions does not reproduce patterns of adaptive clinal differentiation in Drosophila melanogaster
Experimental evolution can be a useful tool for testing the impact of environmental factors on adaptive changes in populations, and this approach is being increasingly used to understand the potential for evolutionary responses in populations under changing climates. However in natural populations selective factors will often be more complex than in laboratory environments and produce different patterns of adaptive differentiation. Here we test the ability for laboratory experimental evolution under different temperature cycles to reproduce well-known patterns of clinal variation in Drosophila melanogaster. Six fluctuating thermal regimes mimicking the natural temperature conditions along the east coast of Australia were initiated. Contrary to expectations based on field patterns there was no evidence for adaptation to thermal regimes as reflected by changes in cold and heat resistance following 1-3 years of laboratory natural selection. While laboratory evolution led to changes in starvation resistance, development time and body size, patterns were not consistent with those seen in natural populations. These findings highlight the complexity of factors affecting trait evolution in natural populations and indicate that caution is required when inferring likely evolutionary responses from the outcome of experimental evolution studies.
Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations
Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey using neutral microsatellites and mitochondrial sequence variation jointly. Thirty-five populations originating from five continents were compared. In agreement with previous microsatellite studies, sub-Saharan African populations were the most variable ones. Consistent with previous reports of a single 'out of Africa' habitat expansion, we found that non-African populations contained a subset of the African alleles. The pattern of variation detected for the mitochondrial sequences differed substantially. The most divergent haplotypes were detected in the Mediterranean region while Africa harbored most haplotypes, which were all closely related. In the light of the well-established African origin of D. melanogaster, our results cast severe doubts about the suitability of mtDNA for biogeographic inference in this model organism.
Data from: Epidermal growth factor receptor and transforming growth factor-ß signaling contributes to variation for wing shape in Drosophila melanogaster
Wing development in Drosophila is a common model system for the dissection of genetic networks and their roles during development. In particular, the RTK and TGF-ß regulatory networks appear to be involved with numerous aspects of wing development, including patterning, cell determination, growth, proliferation, and survival in the developing imaginal wing disc. However, little is known as to how subtle changes in the function of these genes may contribute to quantitative variation for wing shape, per se. In this study 50 insertional mutations, representing 43 loci in the RTK, Hedgehog, TGF-ß pathways, and their genetically interacting factors were used to study the role of these networks on wing shape. To concurrently examine how genetic background modulates the effects of the mutation, each insertion was introgressed into two wild-type genetic backgrounds. Using geometric morphometric methods, it is shown that the majority of these mutations have profound effects on shape but not size of the wing when measured as heterozygotes. To examine the relationships between how each mutation affects wing shape hierarchical clustering was used. Unlike previous observations of environmental canalization, these mutations did not generally increase within-line variation relative to their wild-type counterparts. These results provide an entry point into the genetics of wing shape and are discussed within the framework of the dissection of complex phenotypes.
Data from: Nucleotide variation in the Egfr locus of Drosophila melanogaster
The Epidermal growth factor receptor is an essential gene with diverse pleiotropic roles in development throughout the animal kingdom. Analysis of sequence diversity in 10.9 kb covering the complete coding region and 6.4 kb of potential regulatory regions in a sample of 250 alleles from three populations of Drosophila melanogaster suggests that the intensity of different population genetic forces varies along the locus. A total of 238 independent common SNPs and 20 indel polymorphisms were detected, with just six common replacements affecting >1475 amino acids, four of which are in the short alternate first exon. Sequence diversity is lowest in a 2-kb portion of intron 2, which is also highly conserved in comparison with D. simulans and D. pseudoobscura. Linkage disequilibrium decays to background levels within 500 bp of most sites, so haplotypes are generally restricted to up to 5 polymorphisms. The two North American samples from North Carolina and California have diverged in allele frequency at a handful of individual SNPs, but a Kenyan sample is both more divergent and more polymorphic. The effect of sample size on inference of the roles of population structure, uneven recombination, and weak selection in patterning nucleotide variation in the locus is discussed.
Data from: Phenotypic plasticity in female mate choice behavior is mediated by an interaction of direct and indirect genetic effects in Drosophila melanogaster
Female mate choice is a complex decision-making process that involves many context-dependent factors. In Drosophila melanogaster, a model species for the study of sexual selection, indirect genetic effects (IGEs) of general social interactions can influence female mate choice behaviors, but the potential impacts of IGEs associated with mating experiences are poorly understood. Here, we examined whether the IGEs associated with a previous mating experience had an effect on subsequent female mate choice behaviors and quantified the degree of additive genetic variation associated with this effect. Females from 21 different genetic backgrounds were housed with males from one of two distinct genetic backgrounds for either a short (3 hr) or long (48 hr) exposure period and their subsequent mate choice behaviors were scored. We found that the genetic identity of a previous mate significantly influenced a female's subsequent interest in males and preference of males. Additionally, a hemiclonal analysis revealed significant additive genetic variation associated with experience-dependent mate choice behaviors, indicating a genotype-by-environment interaction for both of these parameters. We discuss the significance of these results with regard to the evolution of plasticity in female mate choice behaviors and the maintenance of variation in harmful male traits.
Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least two of the four genotypes in either males or females or across both sexes. Strikingly, while 25% of all genes differ between the two parents, 33% differ between both F1's and the parents, averaged across sexes. However, only 5% of genes show overdominance, suggesting that heterosis for expression is rare.
Walking behavior of flies (Drosophila melanogaster)
<h3>Dataset description</h3> <p>The dataset consists of walking behaviors of flies, <em>Drosophila melanogaster</em>, that were placed in an acrylic arena that constrained them to move in a 2D plane. The flies were part of a genetic screen (not wild-type) but were examined during behavior capture and were morphologically and behaviorally indistinguishable from wild-type flies.</p> <p>We placed three female flies in one arena simultaneously and filmed them from below for 3 seconds (frame rate 80Hz). This was repeated several times for different sets of flies. To extract each fly from the video separately, we tracked the centroid of each fly using Tracktor (Sridhar et al. 2019), cropped out the flies in each frame, and aligned them to point in the same direction. We then tracked 32 body parts (four joints per leg, as well as head features, thorax, abdomen, and wings), each with x- and y-directions using DeepLabCut (Mathis et al. 2018). This resulted in time series with 64 feature dimensions. We then smoothed the extracted time series using a Savitzky-Golay-Filter (Savitzky and Golay, 1964).</p> <h3>Dataset dimensions</h3> <div> <div> <table> <tbody> <tr> <td>number of sequences</td> <td>28059</td> </tr> <tr> <td>sequence length</td> <td>234</td> </tr> <tr> <td>keypoints (2 per keypoint)</td> <td>64</td> </tr> </tbody> </table> <p> </p> </div> </div> <p>frame rate: 80 Hz </p> <h3>Loading the data in Python</h3> <p> </p> <pre><code>import h5py with h5py.File('Fly_DLC_behavior_tracking.h5', 'r') as f: data = f['data'][:]</code></pre>
Comparison of the secretome of follicle cells during developmental phagoptosis and starvation-induced apoptotic death of nurse cells in Drosophila melanogaster oogenesis.
<p>Associated preprint - https://www.biorxiv.org/content/10.1101/2024.03.12.584558v1</p> <p><strong>Keywords </strong></p> <p>secretome, Drosophila, oogenesis, cell death, HRP-KDEL</p> <p><strong>Sample Processing Protocol</strong></p> <p>pDisplay-ss-V5-HRPKDEL was obtained from Dr. Alice Ting (Stanford).The insert was PCR-amplified and cloned into the pENTR/D-TOPO cloning kit (Invitrogen) and pTW vector (Drosophila Genome Resource Center, RRID:DGRC_1129)) using Gateway cloning (Invitrogen). The plasmid was purified by Qiagen Midiprep kit, confirmed by sequencing and sent to BestGene (Chino Hills, CA) for injection into Drosophila embryos. Freshly dissected ovaries were incubated in 300 μL of 500 uM biotin phenol for 30 minutes at room temperature rotating. Samples were then rinsed with 1X PBS twice and the biotinylation reaction was initiated by adding 1 mM H2O2 in PBS to the samples for 1 minute and rotating at room temperature. Ovaries were quickly washed with quencher solution (10 mM sodium ascorbate, 5 mM Trolox (Sigma-Aldrich), 10 mM sodium azide, then lysed in 100 μL RIPA buffer with quencher solution for 5 min on ice. RIPA buffer was composed of: 50 μL 1M Tris-HCl, 150 μL 5M NaCl, 50 μL of 10% SDS, 250 μL of 10% Sodium Deoxycholate, 500 μL of 10% TritonX-100, 50 μL of 100X Protease Inhibitor (Sigma-Aldrich – P8849), 50 μL of 100 mM PMSF, 3.550 mL of diH20. Tissue was homogenized by motorized pestle and centrifuged at 16.1g for 10 min at 4°C. Clarified sample (clear middle layer) was transferred to a new tube and snap frozen in liquid nitrogen. Biotinylated proteins were pulled down using streptavidin magnetic beads. Beads from biotinylated protein pull-down were washed with 100 mM triethylammonium bicarbonate. Peptides were eluted from beads by on-bead trypsin digestion with 1μg Trypsin (Pierce) in 100 mM triethylammonium bicarbonate overnight rotating at 37°C. Peptides were desalted using C18 ZipTip (Millipore) and subjected liquid chromatography coupled to tandem mass spectrometry on a Q Exactive HF-X (Thermo Fisher Scientific). Data-dependent fragmentation used collision-induced dissociation.</p> <p><strong>Data Processing Protocol</strong></p> <p>RAW files were searched using MaxQuant under standard settings using the UniProt Drosophila melanogaster database, allowing for two missed trypsin cleavage sites, variable modifications for N-terminal acetylation, and methionine oxidation. Candidate peptides and protein identifications were filtered on the basis of a 1% false discovery rate.</p> <p><strong>Experiment Type</strong></p> <p>Data-dependent acquisition</p> <p><strong>Files included</strong></p> <p>MaxQuant search files - <br>tables.pdf<br>allPeptides.txt<br>evidence-mss.txt<br>evidence.txt<br>GlyGly_KSites.txt<br>HRPKDEL_dmel.xlsx<br>libraryMatch.txt<br>matchedFeatures.txt<br>modificationSpecificPeptides.txt<br>ms3Scans.txt<br>msms.txt<br>msmsScans.txt<br>msScans.txt<br>mzRange.txt<br>Oxidation_MSites.txt<br>parameters.txt<br>peptides.txt<br>Phospho_STYSites.txt<br>proteinGroups.txt<br>QQTGG_KSites.txt<br>summary.txt</p>
Data from: The adaptive significance of chromosomal inversion polymorphisms in Drosophila melanogaster
Chromosomal inversions, structural mutations that reverse a segment of a chromosome, cause suppression of recombination in the heterozygous state. Several studies have shown that inversion polymorphisms can form clines or fluctuate predictably in frequency over seasonal time spans. These observations prompted the hypothesis that chromosomal rearrangements might be subject to spatially and/or temporally varying selection. Here we review what has been learned about the adaptive significance of inversion polymorphisms in the vinegar fly Drosophila melanogaster, the species in which they were first discovered by Sturtevant in 1917. A large body of work provides compelling evidence that several inversions in this system are adaptive; however, the precise selective mechanisms that maintain them polymorphic in natural populations remain poorly understood. Recent advances in population genomics, modeling and functional genetics promise to greatly improve our understanding of this longstanding and fundamental problem in the near future.
Contribution of germline to sex-biased expression in Drosophila melanogaster
GEO Series GSE11017. Drosophila melanogaster. 22 samples. Type: Expression profiling by array.
Knockout of Hsp70 genes significantly affects locomotion speed and gene expression in leg skeletal muscles of Drosophila melanogaster
GEO Series GSE239395. Drosophila melanogaster. 40 samples. Type: Expression profiling by high throughput sequencing.
Natural variation in the maternal and zygotic mRNA complements of the early embryo in Drosophila melanogaster
GEO Series GSE195496. Drosophila melanogaster. 48 samples. Type: Expression profiling by high throughput sequencing.
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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.