Ontology highlight
ABSTRACT:
PROVIDER: PRJNA658432 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12642900_1.fastq.gz | Fastqsanger.gz | |||
| SRR12642900_2.fastq.gz | Fastqsanger.gz | |||
| SRR12643000_1.fastq.gz | Fastqsanger.gz | |||
| SRR12643000_2.fastq.gz | Fastqsanger.gz | |||
| SRR12642901_1.fastq.gz | Fastqsanger.gz |
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Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR.
2010-06-16 | GSE19371 | GEO
Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR. 12 Samples, 4 groups 3 samples per group.
2010-06-16 | E-GEOD-19371 | biostudies-arrayexpress
Project description:Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils
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Project description:Background: Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to specific environmental conditions, and may thus be a neuromolecular regulator of both of these processes. A previous study reported DNA methylation differences between aggressive Africanized and gentle European honey bees. We investigated whether threat-induced aggression altered DNA methylation profiles in the honey bee brain in response to a behavioral stimulus (aggression-provoking intruder bee or inert control). We sampled five minutes and two hours after stimulus exposure to examine the effect of time on epigenetic profiles of aggression. Results: There were DNA methylation differences between aggressive and control bees for individual cytosine-guanine dinucleotides (CpGs) across the genome. Eighteen individual CpG sites showed significant difference between aggressive and control bees 120 minutes post stimulus. For clusters of CpGs, we report four genomic regions differentially methylated between aggressive and control bees at the 5-minute time point, and 50 regions differentially methylated at the120-minute time point following intruder exposure. Differential methylation occurred at genes involved in neural plasticity, chromatin remodeling and hormone signaling. Additionally, there was a significant overlap of differential methylation with previously published epigenetic differences that distinguish aggressive Africanized and gentle European honey bees, suggesting an evolutionarily conserved use of brain DNA methylation in the regulation of aggression. Lastly, we identified individually statistically suggestive CpGs that as a group were significantly associated with differentially expressed genes underlying aggressive behavior and also co-localize with binding sites of transcription factors involved in neuroplasticity or neurodevelopment. Conclusions: There were DNA methylation differences in the brain associated with response to an intruder. These differences increased in number a few hours after the initial exposure and overlap with previously reported aggression-associated genes and neurobiologically relevant transcription factor binding sites. Many DNA methylation differences that occurred in association with the expression of aggression in real time also exist between Africanized bees and European bees, suggesting an evolutionarily conserved role for epigenetic regulation in aggressive behavior.
2018-02-13 | GSE104994 | GEO
Project description:There were important gaps in our knowledge of Israeli acute paralysis virus (IAPV), when IAPV was tightly linked to bee Colony Collapse Disorder (CCD), the mysterious disease that, starting in 2006-2007, has been wiping out honey bees in the US. To fill in these gaps we studied the molecular basis of transmission, pathogenesis, and genetic diversity of IAPV infection in honey bees. We investigated the impact of IAPV infection on colony losses and host transcriptional response to IAPV infections, and exploited the potential of RNAi-based strategies for treating viral diseases in honey bees. Our study clearly shows that IAPV has become established as a persistent infection and is highly prevalent in the honey bee population. The existence of both horizontal and vertical transmission pathways of the virus likely accounts for the high prevalence of IAPV in bees. While IAPV is probably not the only culprit responsible for CCD, its ability to cause increased mortality in honey bees is firmly demonstrated. The phenotypic differences in pathology among different strains of IAPV may be due to their high level of standing genetic variation. The JAK-STAT pathway, along with other signaling events such as mTOR and MAPK pathways, likely involves honey bees’ antiviral immune responses to the IAPV infection. The identification of IAPV-encoded putative suppressor of RNAi and evidence that silencing the RNAi suppressor led to a significant reduction in IAPV replication in infected bees illustrates the therapeutic potential of targeting viral suppressor protein to reduce virus replication. Our study gives direction for developing strategies to reduce colony losses due to viral diseases.
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Project description:Phylogenomic analyses of Diptera to resolve long-standing questions in fly classification
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Project description:Phylogenomic analyses of Diptera to resolve long-standing questions in fly classification
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Project description:Phylogenomic analyses of Diptera to resolve long-standing questions in fly classification
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Project description:There were important gaps in our knowledge of Israeli acute paralysis virus (IAPV), when IAPV was tightly linked to bee Colony Collapse Disorder (CCD), the mysterious disease that, starting in 2006-2007, has been wiping out honey bees in the US. To fill in these gaps we studied the molecular basis of transmission, pathogenesis, and genetic diversity of IAPV infection in honey bees. We investigated the impact of IAPV infection on colony losses and host transcriptional response to IAPV infections, and exploited the potential of RNAi-based strategies for treating viral diseases in honey bees. Our study clearly shows that IAPV has become established as a persistent infection and is highly prevalent in the honey bee population. The existence of both horizontal and vertical transmission pathways of the virus likely accounts for the high prevalence of IAPV in bees. While IAPV is probably not the only culprit responsible for CCD, its ability to cause increased mortality in honey bees is firmly demonstrated. The phenotypic differences in pathology among different strains of IAPV may be due to their high level of standing genetic variation. The JAK-STAT pathway, along with other signaling events such as mTOR and MAPK pathways, likely involves honey bees’ antiviral immune responses to the IAPV infection. The identification of IAPV-encoded putative suppressor of RNAi and evidence that silencing the RNAi suppressor led to a significant reduction in IAPV replication in infected bees illustrates the therapeutic potential of targeting viral suppressor protein to reduce virus replication. Our study gives direction for developing strategies to reduce colony losses due to viral diseases. Adult worker bees and brood were collected from colonies that were declining and identified with IAPV infections and its control with 6 replications per group.
2014-04-08 | E-GEOD-46278 | biostudies-arrayexpress