CF-MS experiment in honey bee midgut
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Apis Mellifera (honeybee)
TISSUE(S): Gut
SUBMITTER: 
Mopelola Akinlaja
LAB HEAD: Leonard Foster
PROVIDER: PXD042820 | Pride | 2023-12-11
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 403 |
Similar Datasets
Project description:The honey bee is a key pollinator in many agricultural operations as well as a model organism for studying the genetics and evolution of social behaviour. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant aspects of their biology. One troubling trend that emerged from proteomic analyses is that honey bee peptide samples consistently result in lower peptide identification rates compared to other organisms. This suggests that the genome annotation can be improved, or atypical biological processes are interfering with the mass spectrometry workflow. First, we tested whether high levels of polymorphisms could explain some of the missed identifications by searching spectra against the reference proteome (OGSv3.2) versus a customized proteome of a single honey bee, but our results indicate that this contribution was minor. Likewise, error-tolerant peptide searches lead us to eliminate unexpected post-translational modifications as a major factor in missed identifications. We then used a proteogenomic approach with ~1,500 raw files to search for missing genes, new exons, and revive discarded annotations and identified over 2,000 new coding regions. These results will contribute to a more comprehensive genome annotation and facilitate continued research on this important insect.
2016-01-18 | PXD002275 | Pride
Project description:Honey bee colonies were maintained in an apiary at the University of British Columbia. During the summer of 2018, 40 queens were reared from a single colony and half were allowed to open mate, while the other half were kept as virgins in plastic queen cages. Two weeks after emergence, the virgin queens were given two, eight-minute carbon dioxide treatments on 2 sequential days, then re-introduced to their nucleus colonies. This process stimulates virgin queens to begin laying71, and we conducted these treatments in order to minimize the physiological differences between virgin and mated queens. Virgin and mated queens were retrieved from their nucleus colonies and half of each (10) were subjected to heat-shock (42 ͦC, 2 h), and then maintained at 30 ͦC for 2 d. The other half were held only at 30 ͦC for 2 d. Four to six weeks after mating, the queens were anesthetized with carbon dioxide, beheaded, then their spermathecae (including the tracheal net) were removed with fine forceps. Both ovaries were also removed and weighed. During the same summer, 200 drones from a different colony in the same apiary were collected and maintained in the laboratory overnight at ambient temperature with excess syrup (50% sucrose). The next day, semen was harvested with glass capillaries according to the methods described above. Because many drones were not sexually mature, 60 semen samples (out of the 200 drones) were collected. Capillaries were placed in petri dishes and half (30) were heat-shocked as described above, then kept at 25 ͦC for 2 d. The other half were only kept at 25 ͦC for 2 d. Ten samples from each experimental group were used for sperm viability assays as described above.
2019-07-19 | PXD013728 | Pride
Project description:Here, we examined the transcriptional and epigenetic (DNA methylation) responses to viral infection in honey bee workers. One-day old worker honey bees were fed solutions containing Israeli Acute Paralysis Virus (IAPV), a virus which causes muscle paralysis and death and has previously been associated with colony loss. Uninfected control and infected, symptomatic bees were collected within 20-24 hours after infection. Worker fat bodies, the primary tissue involved in metabolism, detoxification and immune responses, were collected for analysis. We performed transcriptome- and bisulfite-sequencing of the worker fat bodies to identify genome-wide gene expression and DNA methylation patterns associated with viral infection. There were 753 differentially expressed genes (FDR<0.05) in infected versus control bees, including several genes involved in epigenetic and antiviral pathways. DNA methylation status of 156 genes (FDR<0.1) changed significantly as a result of the infection, including those involved in antiviral responses in humans. There was no significant overlap between the significantly differentially expressed and significantly differentially methylated genes, and indeed, the genomic characteristics of these sets of genes were quite distinct. Our results indicate that honey bees have two distinct molecular pathways, mediated by transcription and methylation, that modulate protein levels and/or function in response to viral infections. Examination of epigenomic and transcriptomic antiviral responses to Israeli Acute Paralysis Virus in honey bees
2015-02-06 | E-GEOD-65659 | biostudies-arrayexpress
Project description:Pathogen detection microarrays analyzing honeybee samples taken after parasitization with a predatory fly, oligos correspond to specific pathogens or pathogen families of viruses, bacteria, fungi, protists, and other parasites Samples were analyzed with the E-Predict analysis package. Honey bees parasitized with the phorid fly Apocephalus borealis were screened for viral and non-viral pathogens by microarray.
2012-07-31 | E-GEOD-29749 | biostudies-arrayexpress
Project description:Mating is a complex process, which is frequently associated with behavioural and physiological changes. However, understanding of the genetic underpinnings of these changes is limited. Honey bees are both a model system in behavioural genomics, and the dominant managed pollinator of human crops; consequently understanding the mating process has both pure and applied value. We used next-generation transcriptomics to probe changes in gene expression in the brains of honey bee queens, as they transition from virgin to mated reproductive status. In addition, we used CO2-narcosis, which induces oviposition without mating, as an experimental control for the mating process. Mating produced significant changes in the expression of vision, chemo-reception, metabolic, and immune-related genes. Differential expression of these genes maps clearly onto known behavioural and physiological changes that occur during the transition from being a virgin queen to a newly-mated queen. A subset of these changes in gene expression were also detected in CO2-treated queens, as predicted from previous physiological studies. In addition, we compared our results to previous studies that used microarray techniques across a range of experimental time-points. Changes in expression of immune- and vision-related genes were common to all studies, supporting an involvement of these groups of genes in the mating process. However, these comparisons also indicate the need to understand the temporal dynamics of gene expression across the entire mating and reproductive process. Brain RNA samples for 3 treatments: control (N=4), mated (N=4) and treated with carbon dioxide (N=4)
2015-09-23 | E-GEOD-65833 | biostudies-arrayexpress
Project description:Honey promotes health and is an effective non-pharmacological home remedy against common respiratory infections. However, industrial processing and manipulation of raw honey can have a detrimental effect on its biological activities, including antibacterial ones, and hence its health-benefiting qualities. Therefore, this study aimed to compare the honey’s antibacterial activity, its total protein content, and the abundance of the most dominant bee-derived proteins in honey between raw (n=92) and supermarket (n=17) samples. We showed that raw honey samples were much more effective in inhibiting the growth of Staphylococcus aureus with a median minimal inhibitory concentration (MIC) value of 4.5% compared to supermarket honey samples ceasing bacterial growth with a median MIC value of 36%. Moreover, raw honey samples contained significantly higher amounts of total protein as well as the content of particular bee-derived proteins (major royal jelly protein 1 (MRJP1), glucose oxidase (GOX), and α-glucosidase) in contrast to supermarket honey samples. These data hint that some marketed honey samples could be deliberately manipulated with syrup, especially those that exhibited low protein content. In addition, the supermarket honey sample with the lowest protein content contained α-amylase (diastase) from Aspergillus oryzae. Strikingly, the content of this foreign enzyme in honey was roughly 60 times higher than the naturally occurring bee α-amylase. Our findings highlight the burning need to refine and monitor the specific quality parameters, ensuring the authenticity of honey and maintaining its reputation as a functional food.
2023-08-12 | PXD040190 | Pride
Project description:Sexual reproduction brings genes from two parents â matrigenes and patrigenes â into one individual. These genes, despite being unrelated, should show nearly perfect cooperation because each gains equally through production of offspring. However, an individualâs matrigenes and patrigenes can have different probabilities of being present in other relatives, so that kin selection could act on them differently. Such intragenomic conflict could be implemented by partial or complete silencing (imprinting) of an allele by one of the parents. Evidence supporting this theory is seen in offspring-mother interactions, with patrigenes favoring acquisition of more of the mother's resources if some of the costs fall on half siblings who do not share the patrigene. The kinship theory of intragenomic conflict is little tested in other contexts, but it predicts that matrigene-patrigene conflict may be rife in social insects. We tested the hypothesis that honey bee worker reproduction is promoted more by patrigenes than matrigenes by comparing across 9 reciprocal crosses of two distinct genetic stocks. As predicted, hybrid workers show reproductive trait characteristics of their paternal stock, indicating enhanced activity of the patrigenes on these traits, greater patrigenic than matrigenic expression, and significantly increased patrigenic biased expression in reproductive workers. These results support both the general prediction that matrigene-patrigene conflict occurs in social insects and the specific prediction that honey bee worker reproduction is driven more by patrigenes. The success of these predictions suggests that intragenomic conflict may occur in many contexts where matrigenes and patrigenes have different relatednesses to affected kin. Testing the kinship theory of intragenomic conflict in honey bees
2015-12-19 | E-GEOD-76164 | biostudies-arrayexpress
Project description:Honey bee drones, queens and workers have vastly different phenotypes. Here we profile the the expression level of mRNAs and microRNAs of honeybee, drones, queens and workers at the L5 larval stage (91 hours +/- 1).
2015-09-06 | GSE61253 | GEO
Project description:Pathogen detection microarrays analyzing honeybee samples taken from the same hives over the course of a year, oligos correspond to specific pathogens or pathogen families of viruses, bacteria, fungi, protists, and other parasites Samples were analyzed with the E-Predict analysis package Twenty hives samples biweekly, Timepoint refers to sample collection week after start, where T01 refers to April 15, 2009. Hive refers to the specific hive sampled.
2011-06-06 | E-GEOD-28235 | biostudies-arrayexpress
Project description:Our molecular understanding of honey bee cellular stress responses is incomplete. Previously, we sought to identify and began functional characterization of the components of the UPR in honey bees. We observed that UPR stimulation resulted in induction of target genes upon and IRE1 pathway activation, as assessed by splicing of Xbp1 mRNA. However, were not able to determine the relative role of the various UPR pathways in gene activation. Our understanding of honey bee signal transduction and transcriptional regulation has been hampered by a lack of tools. After using RNAseq to expand the known UPR targets in the bee, we use the Drosophila melanogaster S2 cell line and honey bee trans and cis elements to investigate the role of the IRE-1 pathway in the transcriptional activation of one of these targets, the honey bee Hsc70-3 gene. Using a luciferase reporter, we show that honey bee hsc70 promoter activity is inducible by UPR activation. In addition, we show that this activation is IRE1-dependent and relies on specific cis regulatory elements. Experiments using exogenous honey bee or fruit fly XBP1S proteins demonstrate that both factors can activate the Hsc70-3 promoter and further support a role for the IRE-1 pathway in control of its expression in the honey bee. By providing foundational knowledge about the UPR in the honey bee and demonstrating the usefulness of a heterologous cell line for molecular characterization of honey bee pathways, this work stands to improve our understanding of this critical species.
2020-03-28 | GSE139368 | GEO