Title Multi-generational mRNA sequence data of pooled Drosophila melanogaster male and female flies from populations selected for long or short night sleep
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PROVIDER: PRJNA836753 | ENA |
REPOSITORIES: ENA
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Project description:Our objective was to determine whether gene expression in Drosophila melanogaster selectively bred for long or short night sleep duration changes detectably across generations. To meet this objective, we performed transcriptional profiling of ten pooled whole adult individuals from four selected populations and two control populations across 13 generations. We quantified differential expression among selection scheme (long sleep, short sleep, or unselected control), generation (generation 0; then generations 2-13), and sex for each gene.
2023-07-29 | GSE202600 | GEO
Project description:We investigated sleep deficits in Cyfip mutant Drosophila flies, a model for intellectual disabilities/neurodevelopmental disorders. RNA-seq was performed on heads at the circadian time point ZT16, i.e., during the night when wild-type flies are asleep.
2022-12-11 | GSE220524 | GEO
Project description:Study Objectives: Sleep deprivation is highly prevalent and caused by conditions such as night shift work or illnesses like obstructive sleep apnea. Compromised sleep is proposed to play a role in several cardiovascular, immune related and neurodegenerative disorders. We recently published human serum proteome changes after a simulated night shift. This study aimed to further explore changes in the human blood serum after 6h of sleep deprivation at night by proteomics and systems biological databases. Methods: Human blood serum samples from 8 self-declared healthy females were analyzed using mass spectrometry and high-pressure liquid chromatography. Each subject was their own control, and two samples were taken from each subject, the first one after 6h of sleep at night and the second one after 6h of sleep deprivation the following night. Biological databases and bioinformatic software were used for systems biological analyzes and comparative analysis with other published sleep-related datasets. Results: Of 494 proteins, 66 were found to be differentially expressed after 6h of sleep deprivation at night. Functional enrichment analysis revealed associations of these proteins with several biological functions related to the regulation of cellular processes like protein- and ion-binding connected to platelet degranulation and blood coagulation, as well as associations with different curated gene sets. Conclusions: This study presents serum proteomic changes after 6h of sleep deprivation, supports previous findings that only 6h of sleep deprivation affects several biological processes and revealed a molecular signature of protein changes related to pathological conditions like altered coagulation and platelet function, impaired lipid and immune function and cancer. Keywords: Human blood serum, proteomics, sleep deprivation, cellular stress, functional enrichment analysis
2024-06-27 | PXD045729 | Pride
Project description:Tsetse flies (Glossina spp.) are major vectors of African trypanosomes, causing either Human or Animal African Trypanosomiasis (HAT or AAT). Several approaches are developed to control the disease among which the anti-vector Sterile Insect Technique. Another approach in the frame of anti-vector strategies could consist in controlling the fly’s vector competence which needs identifying factors (genes, proteins, biological pathways, …) involved in this process. The present work aims to verify whether protein candidates identified under experimental controlled conditions on insectary-reared tsetse flies have their counterpart in field-collected flies. Glossina palpalis palpalis flies naturally infected with Trypanosoma congolense were sampled in two HAT/AAT foci in Southern Cameroon. After dissection, the proteome from guts of parasite-infected flies were compared to that from uninfected flies in order to identify quantitative and/or qualitative changes associated to infection. A total of 3291 proteins were identified of which 1818 could be quantified. The comparative analysis allowed identifying 175 proteins with significant decreased abundance in infected as compared to uninfected flies, while 61 proteins displayed increased abundance. Among the former are RNA binding proteins, kinases, actin, ribosomal proteins, endocytosis proteins, oxido-reductases, as well as proteins that are unusually found such as tsetse salivary proteins (Tsal) or Yolk proteins. Among the proteins with increased abundance are fructose-1,6-biphosphatase, serine proteases, membrane trafficking proteins, death proteins (or apoptosis proteins), and SERPINs (inhibitor of serine proteases, enzymes considered as trypanosome virulence factors) that displayed highest increased abundance. Sodalis, Wiggleswothia and Wolbachia proteins are strongly under-represented, particularly when compared to data from similar experimentation conducted under controlled conditions on T. brucei gambiense infected (or uninfected) G. palpalis gambiensis insectary reared flies. Comparing the overall recorded data, 364 proteins identified in gut extracts from field flies were shown to have a homologue in insectary flies. Discrepancies between the two studies may arise from differences in the species of studied flies and trypanosomes as well as in differences in environmental conditions in which the two experiments were carried out. Finally, the present study together with former proteomic and transcriptomic studies on the secretome of trypanosomes, on the gut extracts from insectary reared and on field collected tsetse flies, provide a pool of data and information on which to draw in order to perform further investigations on, for example, mammal host immunization or on fly vector competence modification via para-transgenic approaches.
2023-07-26 | PXD034619 | Pride
Project description:In order to investigate the functional relevance of SUR2 (the protein encoded by ABCC9 in humans) for sleep duration, we knocked down the expression of its Drosophila homologue (dSur) in the flies’ nervous system (both central and peripheral). Unlike humans, flies are active predominantly around dawn and dusk and show two large sleep episodes during the day and during the night. Knockdown of dSur dramatically reduced night-sleep, particularly during the first half of the dark period, but had little effect on the flies’ day-sleep. This was true for both elavgal4 UAS-Sur RNAi genotypes compared with their parental control strains. These differences in sleep duration were not due to changes in the circadian clock, as the period of the free-running locomotor activity rhythm in constant darkness was indistinguishable between knockdown flies and controls. Furthermore, no systematic differences in activity levels were found between experimental genotypes and control. Thus, the major effect of knocking down the ABCC9 homologue in flies is shortening nighttime sleep due to a delay of its onset by 3 h.
2018-03-08 | GSE52764 | GEO
Project description:Microarray data obtained from control, cbtRNAi (cabut RNAi), and cbtOE (cabut overexpression) flies. From each strain, fly heads at two different time points during the day–night cycle (ZT3 and ZT153) were collected. Fly heads were collected and RNA was extracted. RNA was then used to prepare a probe that was hybridized to Drosophila 2.0 gene expression arrays (Affymetrix). Two samples of cbtRNAi, two samples of cbtOE and two samples of the control flies (cyo).
2015-05-08 | E-GEOD-67865 | biostudies-arrayexpress
Project description:The aim of this study was to discover significantly changed proteins in human blood serum as a result of 6 h sleep loss at night. Eight females were reqruited. . Peripheral venous whole blood sampling was performed at 04:00, after 6 h of sleep and after 6 h of sleep deprivation (SD). Serum from each subject was depleted before protein digestion by trypsin and iTRAQ labeling. Labled peptides were analyzed by mass spectrometry.
2023-09-26 | PXD021004 | Pride
Project description:Extended periods of waking result in physiological impairments in humans, rats, and flies. Sleep homeostasis, the increase in sleep observed following sleep loss, is believed to counter the negative effects of prolonged waking by restoring vital biological processes that are degraded during sleep deprivation. Sleep homeostasis, as with other behaviors, is influenced by both genes and environment. We report here that during periods of starvation, flies remain spontaneously awake but, in contrast to sleep deprivation, do not accrue any of the negative consequences of prolonged waking. Specifically, the homeostatic response and learning impairments that are a characteristic of sleep loss are not observed following prolonged waking induced by starvation. To identify the genes responsible for the protective effects of starvation we conducted transcription profiling of sleep deprived flies that accrue sleep debt compared to starved siblings that do not. Genes involved in lipid metabolism were highly enriched in our dataset of 84 differentially regulated transcripts. Follow up genetic studies established that 6 genes involved in lipid metabolism strongly influence sleep homeostasis. Two of these genes, brummer (bmm) and Lipid storage droplet 2 (Lsd2), are in the same lipolysis pathway but exert antagonistic effects on lipid storage. bmm mutant flies have excess fat stores and display a large homeostatic response following sleep deprivation. In contrast, Lsd2 mutant flies, which phenocopy aspects of starvation as measured by low triglyceride stores, do not exhibit a homeostatic response following sleep loss. Importantly, Lsd2 mutant flies are not learning impaired after sleep deprivation. These results provide the first genetic evidence, to our knowledge, that lipid metabolism plays an important role in regulating the homeostatic response and can protect against neuronal impairments induced by prolonged waking. Two-condition experiments: sleep deprived vs starved. RNA from 8 biological replicates for each condition was pooled in groups of 2 to create 4 samples. Each of the 4 samples is run in duplicate with untreated circadian matched controls.
2014-04-15 | E-GEOD-18550 | biostudies-arrayexpress
Project description:Microarray data obtained from control, cbtRNAi (cabut RNAi), and cbtOE (cabut overexpression) flies. From each strain, fly heads at two different time points during the day–night cycle (ZT3 and ZT153) were collected. Fly heads were collected and RNA was extracted. RNA was then used to prepare a probe that was hybridized to Drosophila 2.0 gene expression arrays (Affymetrix).
2015-05-08 | GSE67865 | GEO
Project description:Obesity is a global health concern affecting over 650 million adults with a major contributor being an increased consumption of a high-fat diet. Maternal obesity often results in an increased risk of offspring developing obesity. In this study, we examined the effect of diet on visceral adipose in a pre-clinical model of generational diet-induced obesity that included maternal cohorts of C57BL/6 mice fed either a control diet (10% fat) or a high-fat diet (45% fat) and the resulting female offspring fed either diet. Using bottom-up proteomics on omental adipose tissue, differential protein expression was determined with the greatest difference resulting from the generational obese cohort. Differentially expressed proteins were involved in pathways related to cancer, inflammatory disease and immune response. Taken together, the results of this study provide molecular-level insight that will enable the development of more targeted, modifiable interventions that could be implemented pre-, during and post-pregnancy.
2024-10-17 | PXD042092 | Pride