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opencc-by-4.0Jul 2024View details →

Lifespan Fecundity data for The Combined Effects of Macronutrient Ratios and the chico1 Variant on Life History Traits in Drosophila melanogaster

Data sheets for Lifespan Fecundity data for The Combined Effects of Macronutrient Ratios and the chico1 Variant on Life History Traits in Drosophila melanogaster. Chico_life_extention_ds and Chico_CP_life_extention_REP_ds are data sheets from project one that keep track of deaths that occurred in the experiment.  Deaths of males, deaths of females, and censors were recorded. Hour = hour of collection, Minute = minute of collection, Days_alive = number of days flies have been inside the vials after initial collection, last_flip = day of last time flies were flipped, Label = id of the vial, repl = replicant group, deadF = number of females that died before that days collection, deadM = number of males that died before each collection, cens = number of censors before each collection, counter = person who counted the flies, Year = year of collection, Month = month of collection, Day = day of collection, notes = observations during collection.  LDF_flipping_and_counting_data is a data sheet keeping track of deaths that occured in project two. Deaths of females, males, and censors were recorded. Month = month of collection, Day = day of collection, Year = year of collection, Days_alive = number of days flies have been inside vials, Flipped = were the flies flipped with Y meaning Yes and N meaning No, flipper = person who flipped the flies, DeadF = number of dead females before collection, DeadM = number of dead males before collection, Censor = number of censors before collection, Hour = hour of collection, Minute = minute of collection, Label = id of the vial, Notes = observations during collection. LDF_egg_counting_data is a data sheet keeping track of the number of eggs counted on every image in experiment 2. Image_ID i= image identification number, Label = id of the vial, Day = day of collection, Month = month of collection, Year = year of collection, Counter  = person who counted the eggs, Egg_total = number of eggs counted on the photo, notes = observations during collection. Images.zip is a zipped folder of all images that were used to count the number of eggs laid over a ~16-hour time period once per week until the death of all flies in the vial. These images are organized by the date the picture was taken. These pictures were counted using the cell counter extension for ImageJ and counted. Counts were recorded in the LDF_egg_counting_data data sheet.

opencc-by-4.0Aug 2024View details →

Analyses of metabolite profiling of Drosophila Parkinson's Disease model for identifying novel glial-based therapeutic targets

Analysis for genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson’s disease This project contains the analysis of metabolite abundance measurements obtained with four different liquid chromatography mass spectrometry methods of synuclein expressing or control or fly brains in a wilde type or Adk1 knockout background.   <div> <h2>Table of contents</h2> <a href="https://github.com/jravilap/Olsen_Analyses#table-of-contents"></a></div> <div> <h3>Prerequisites</h3> <a href="https://github.com/jravilap/Olsen_Analyses#prerequisites"></a></div> <ul> <li>R (version 4.3.1 or higher)</li> <li>RStudio (optional, but recommended)</li> </ul> <div> <h3>R Packages</h3> <a href="https://github.com/jravilap/Olsen_Analyses#r-packages"></a></div> The following R packages are required. You can install them using the commands below: <div> <pre>install.packages(c("readxl", "calibrate", "dplyr", "ggplot2"))</pre> <div> </div> </div> <div> <h3>Package versions</h3> <a href="https://github.com/jravilap/Olsen_Analyses#package-versions"></a></div> <ul> <li>ggplot2_3.5.1</li> <li>dplyr_1.1.4</li> <li>yaml_2.3.8</li> <li>calibrate_1.7.7</li> <li>readxl_1.4.3</li> </ul> <div> <h2>Project Structure</h2> <a href="https://github.com/jravilap/Olsen_Analyses#project-structure"></a></div> <ul> <li><code>code/</code>: Contains the R scripts for the analysis.</li> <li><code>data/</code>: Processed data files. <ul> <li><code>22_0322_alphaSyn_fly_pilot_Classes.xlsx</code>: metabolite profiling data</li> <li><code>dup_metabs_decision.csv</code>: Table defining which metabolites profiled in more than one method should be used.</li> </ul> </li> <li><code>results/</code>: Output files, including plots and tables.</li> <li><code>common_functions/</code>: Custom R functions used in the analysis.</li> <li><code>config.yml</code>: Configuration file for setting paths.</li> </ul>

opencc-by-4.0Jul 2020View details →

(07)-Ratke2020A-DS0003 – Drosophila melanogaster w[*]; P{w[+mC]=His2Av-EGFP.C}2/SM6a line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(07)-Ratke2020A-DS0003 – Drosophila melanogaster w[*]; P{w[+mC]=His2Av-EGFP.C}2/SM6a line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

opencc-by-4.0Jul 2020View details →

(07)-Ratke2020A-DS0001 – Drosophila melanogaster y[1] w[67c23]; P{w[+mC]=Ubi-GFP.nls}ID-2; P{Ubi-GFP.nls}ID-3 line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(07)-Ratke2020A-DS0001 – Drosophila melanogaster y[1] w[67c23]; P{w[+mC]=Ubi-GFP.nls}ID-2; P{Ubi-GFP.nls}ID-3 line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

opencc-by-4.0Jul 2020View details →

(07)-Ratke2020A-DS0002 – Drosophila melanogaster w[*]; P{w[+mC]=Tub84B-EGFP.NLS}3 long-term live imaging dataset acquired with light sheet fluorescence microscopy

(07)-Ratke2020A-DS0002 – Drosophila melanogaster y[1] w[67c23]; P{w[+mC]=Ubi-GFP.nls}ID-2; P{Ubi-GFP.nls}ID-3 (Bloomington Drosophila Stock Center #29724) long-term live imaging dataset acquired with light sheet fluorescence microscopy

Dataset for: Dopamine neurons that inform Drosophila olfactory memory have distinct, acute functions driving attraction and aversion

The brain must guide immediate responses to beneficial and harmful stimuli while simultaneously writing memories for future reference. While both immediate actions and reinforcement learning are instructed by dopamine, how dopaminergic systems maintain coherence between these two reward functions is unknown. Through optogenetic activation experiments, we showed that the dopamine neurons that inform olfactory memory in Drosophila have a distinct, parallel function driving attraction and aversion (valence). Sensory neurons required for olfactory memory were dispensable to dopaminergic valence. A broadly projecting set of dopaminergic cells had valence that was dependent on dopamine, glutamate, and octopamine. Similarly, a more restricted dopaminergic cluster with attractive valence was reliant on dopamine and glutamate; flies avoided opto-inhibition of this narrow subset, indicating the role of this cluster in controlling ongoing behavior. Dopamine valence was distinct from output-neuron opto-valence in locomotor pattern, strength, and polarity. Overall our data suggest that dopamine’s acute effect on valence provides a mechanism by which a dopaminergic system can coherently write memories to influence future responses while guiding immediate attraction and aversion.

opencc-zeroJan 2024View details →

Linked collectors and determiners for: Drosophila (Sophophora) carrolli n. sp., a new species from Brunei, closely related to Drosophila (Sophophora) rhopaloa Bock & Wheeler, 1972 (Diptera: Drosophilidae).

Natural history specimen data linked to collectors and determiners held within, "Drosophila (Sophophora) carrolli n. sp., a new species from Brunei, closely related to Drosophila (Sophophora) rhopaloa Bock & Wheeler, 1972 (Diptera: Drosophilidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/080903f9-fb09-4979-ab23-db718283e177">https://bionomia.net/dataset/080903f9-fb09-4979-ab23-db718283e177</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/080903f9-fb09-4979-ab23-db718283e177">https://gbif.org/dataset/080903f9-fb09-4979-ab23-db718283e177</a>. Formatted as a Frictionless Data package.

Different effects of Drosophila suzukii oviposition and larval activity on fruit rot and mold

Understanding symbioses and the selective pressures on symbionts requires elucidating how the different behaviors and phenotypes of hosts affect microbes. When female fruit-flies of the genus Drosophila deposit their eggs, they trigger substantial rots (i.e. the development of yeasts and bacteria) and molds (i.e. the development of filamentous fungi). It is however unknown whether these microbial growths are due to female oviposition per-se, or the activity of the larvae that emerge from the eggs. We investigated the specific effects of Drosophila suzukii (Diptera: Drosophilidae) female oviposition and larval activity on rot and mold development in fresh, on-plant strawberry and raspberry. To disentangle the effects of egg deposition from that of larval presence some females were mated with sterile males, as occurs when the Sterile Insect Technique (SIT) is deployed.   This “sterile treatment” without larvae produced intermediate intensities of rot and mold development, greater than “controls” unexposed to flies, but lower than the “fertile treatment” exposed to fertile flies. The proportion of berries too rotten for market access 3 days post-exposure was however equivalent in the sterile and the fertile treatments. But mold after 3 days was only pervasive in the fertile treatment and on strawberry. These results show specific effects of oviposition and larval activity on the development of yeast, bacteria and molds. The study indicates that when D. suzukii females are present in the field, damages to crops cannot be reduced by the release of sterile males. Instead, the sterile insect technique should be used to prevent population build-up.

Winter fruit contribution to the performance of the invasive fruit fly Drosophila suzukii under different thermal regimes

<div> <div> <div> <div> These datasheets and code were used for analyses and to produce the graphics of the article This dataset was used for analyses of the article 'Winter fruit contribution to the performance of the invasive fruit fly Drosophila suzukii under different thermal regimes' submitted for publication in Insect Science. Informations about the datasheet are in 'README and metadata' file. </div> </div> </div> </div>

Life stage-specific effects of heat stress on spermatogenesis and oogenesis in Drosophila melanogaster

#Life stage-specific effects of heat stress on spermatogenesis and oogenesis in Drosophila melanogaster ##Authors Abhishek Meena, Alessio N. De Nardo, Komal Maggu, Sonja Sbilordo, Benjamin Eggs, Rawaa Al Toma Sho, Stefan Lüpold ## Citation of associated article Meena, A., Maggu, K., De Nardo, A.N., Sbilordo, S.H., Eggs, B., Al Toma Sho, R., Lüpold, S., 2024. Life stage-specific effects of heat stress on spermatogenesis and oogenesis in Drosophila melanogaster. Journal of Thermal Biology 125, 104001. https://doi.org/10.1016/j.jtherbio.2024.104001   ##Overview This dataset was collected to assess the impact of heat stress across various life stages on reproductive performance in Drosophila melanogaster.  The study focuses on stage- and sex-specific reproductive metrics such as: mating success, fertility, fecundity, hatching success, which for females were summed over four days and for males were assayed for four consecutive 24-hour periods, each with a different female.  The dataset is structured to analyze these outcomes at different temperatures and developmental stages, providing insights into sex- and stage-specific vulnerabilities to heat stress.  The analyses are performed in an R Markdown (.Rmd) file, using data stored in a CSV file ##Contents The dataset includes the following files: Rscript.Rmd: An R Markdown file containing code for analyzing sex- and stage-specific reproductive fitness based on the data in Data.csv. Data.csv: A CSV file with the raw data used for the analysis. ##Data Description Note: NA's in each data file represent missing data (data not available).  The Data.csv file contains the following columns: Unique.ID: Unique identifier for each experimental individual. SampleID: Identifier for each treatment group. Temperature: Thermal exposure temperature (measured in degrees Celsius) for 4 hours, with levels: 24.5°C, 28°C, 32°C, 36°C, and 38°C. Lifestage: Developmental stage during which thermal treatment was applied. Sex: Sex of the individual exposed to the thermal treatment. Day: Days post adult treatment exposure. Block: Experimental block identifier for randomized grouping. Total: Total number of eggs laid within 24 hours of oviposition. Hatched: Number of eggs that successfully hatched. Unhatched: Number of eggs that did not hatch (derived from the difference between Total and Hatched). ##Usage To analyze the dataset, open and run the respective R Markdown (Rmd) files in RStudio or any compatible R Markdown environment. The Rmd files contain all the necessary code to reproduce the analyses described in the overview.

opencc-by-4.0Nov 2019View details →

Dataset 'Influence of bacteria on the maintenance of a yeast during Drosophila melanogaster metamorphosis'

Dataset from the manuscript 'Influence of bacteria on the maintenance of a yeast during Drosophila melanogaster metamorphosis'

dryad40/100

Physiological data and R script for running physiology combined model for Drosophila suzukii

This is the dataset that accompanies an article entitled "The use of insect life tables in optimizing invasive pest distributional models" that would be published in Ecography. The dataset include two R script that used to generate physical model and the physiology combined model respectively. Our paper shows that the physiology combined model show good performance when applying ecological niche model in risk assessment. We addressed this by determining whether incorporating physiological data from life table analyses of an invasive insect, Drosophila suzukii, improved predictions of ecological niche models. The dataset also include the physiology data D. suzukii that we assembled for running our physiology combined model.

opencc-zeroJul 2021View details →

opencc-by-4.0Jul 2021View details →

Sensory processing during sleep in Drosophila melanogaster - ethoscope dataset

Dataset for "Sensory processing during sleep in Drosophila melanogaster" by French et al Nature 2021 Gilestro Laboratory, Imperial College London https://lab.gilest.ro

dryad40/100

P-elements strengthen reproductive isolation within the Drosophila simulans species complex

Determining mechanisms that underlie reproductive isolation is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of reproductive isolation between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause reproductive isolation between PE-containing (P) and PE-lacking (M) lineages of the same species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P-D. simulans father and an M-mother from a sister species exhibit lower F1 female fecundity than crosses involving an M-D. simulans father and an M-sister-species mother. We also find that another TE, I-element, might play a minor role on determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in isolation. --

opencc-zeroJul 2021View details →

Figures 89–91 in New Species in the Drosophila ananassae Subgroup from Northern Australia, New Guinea and the South Pacific (Diptera: Drosophilidae), with Historical Overview

Figures 89–91. Female oviposcapt (ovipositor) and setation of sixth abdominal tergite of Drosophila ananassae, D. pandora, D. anomalata and D. ironensis. Oviscapt form and colour: (89) Drosophila ananassae ex strain Schiffer CBR57 from Lake Placid; (90) D. pandora sp.nov. ex type strain Schiffer CAQ408 from Lake Placid; (91) D. anomalata sp.nov. ex type strain Schiffer CHC221 from near Deeragun, W of Townsville. Setation of sixth abdominal tergite: (92) D. ananassae ex strain Schiffer CBR54; (93) D. anomalata sp.nov. ex type strain; (94, 95) Drosophila ironensis ♀ and ♂ ex strain Schiffer CHH18 from Lake Placid, note the irregualr orientation of T6 setation in D. ironensis comparaed to the caudally oriented setation in other figured species; and (96) D. pandora sp.nov. ♂ ex type strain. All to same scale.

Figures 78–81 in New Species in the Drosophila ananassae Subgroup from Northern Australia, New Guinea and the South Pacific (Diptera: Drosophilidae), with Historical Overview

Figures 78–81. Hypandria of Drosophila anomalata sp.nov. three males from the type strain Schiffer CHC221 (ventral views); (81) dorsal view of hypandrium in Fig. 80.

Figures 54–71 in New Species in the Drosophila ananassae Subgroup from Northern Australia, New Guinea and the South Pacific (Diptera: Drosophilidae), with Historical Overview

Figures 54–71. Male fore-leg and sex comb of tarsomere I (metatarsus or basitarsus), tarsomere II and III of Drosophila pandora sp.nov. (54–59), D. ananassae (60–65) (from strains established by Schiffer at Lake Placid, northern Queensland) and D. schugi sp.nov. (66–71). Drosophila pandora sp.nov. (54–55) from iso-♀ strain CAR274 [the teeth of the sex comb in Fig. 51 are artificially enhanced and represented schematically to indicate how they are scored]; (56–57) from type strain = iso-♀ strain CAQ408; and (58–59) from iso-♀ strain CAQ425. Drosophila ananassae (60–61) from iso-♀ strain CBR57; (62–63) from iso-♀ strain CBR54; and (64–65) from iso-♀ strain CBR52. Drosophila schugi sp.nov. wild caught males from Malololelei, Upolu, Samoa, 14–17 June 2003, Schug, Gray-Smith, Kilon-Attwood, McEvey; AMS K356978 (66), AMS K356979 (67–68), AMS K356977 (69), and AMS K356976 (70–71).

Figures 26–37 in New Species in the Drosophila ananassae Subgroup from Northern Australia, New Guinea and the South Pacific (Diptera: Drosophilidae), with Historical Overview

Figures 26–37. Hypandria of Drosophila ananassae complex species. Drosophila ananassae (26) 1.5 km NW Taipivai, Nuku Hiva, Marquesas Islands; (27) Belvédère 250 m, fruit bait, Moorea, Society Islands, French Polynesia. Drosophila ananassae or D. pallidosa (28) Sigatoka, 35 km S Nadi, Fiji; (29) Apia, Samoa. Drosophila pallidosa (30) det. by?Wheeler, Pago Pago, ... [continued on facing page]

Figures 38–53 in New Species in the Drosophila ananassae Subgroup from Northern Australia, New Guinea and the South Pacific (Diptera: Drosophilidae), with Historical Overview

Figures 38–53. Epandria of Drosophila ananassae complex species. Drosophila pandora sp.nov. (38) Lake Placid type strain CAQ408, lateral view; (39) type strain CAQ408, caudal view; (40) Lake Placid strain CAR274; (41) Lake Placid strain CAQ425. Drosophila ananassae (42) Beach Lane, Mauritius, Oct. 2012, J. Tann. Drosophila?ananassae (43) Kuranda, northern Queensland, AMS K275429; (44) Sigatoka, 35 km S Nadi, Fiji, AMS K275290; (45) Iron Range, fruit bait, 30.iv.1976, I.R. Bock, [possibly pinned on this date from a strain collected with P.A. Parsons in November 1975—there is no evidence that Bock returned to Iron Range in 1976], AMS K119308 (det. Drosophila ananassae by Bock in 1976). Drosophila pandora sp.nov.: (46) D. "papuensis-like" Kyorin University stock k-aat001, Townsville, Queensland. Drosophila pallidosa: (47) det. by?Wheeler, Pago Pago, American Samoa, Drosophila Species Stock Center (San Diego), stock 14024-0433.01. Drosophila ananassae or D. pallidosa (48) Sigatoka, 35 km S Nadi, Fiji, June 2004, Schug, Gray-Smith, Kilon-Attwood, McEvey, AMS K282851. Drosophila schugi sp.nov. (49) Malololelei, Upolu, Samoa, 14–17 June 2003, paratype AMS K282923. Drosophila anomalata sp.nov. (50–52) ex type strain, Schiffer CHC221. Drosophila schugi sp.nov. (53) Malololelei, Upolu, Samoa, 14–17 June 2003, AMS K356977. Localities—see Fig. 1 and Appendix 1; all specimens in Australian Museum.

Figures 72–77 in New Species in the Drosophila ananassae Subgroup from Northern Australia, New Guinea and the South Pacific (Diptera: Drosophilidae), with Historical Overview

Figures 72–77. Male fore-leg and sex comb of tarsomere I (metatarsus) and II of Drosophila anomalata sp.nov. ex type strain CHC221, nr Deeragun, 16 km W of Townsville. Legs from five males; (73–74) left and right legs from one male [(74) image flipped].