Ontology highlight
ABSTRACT:
PROVIDER: PRJNA566328 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10143177_1.fastq.gz | Fastqsanger.gz | |||
| SRR10143177_2.fastq.gz | Fastqsanger.gz |
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Project description:Cashew is one of the most prevalent causes of tree nut allergies. However, the cashew proteome is far from complete, which limits the quality of peptide identification in mass spectrometric analyses. In this study, bioinformatics tools were utilized to construct a customized cashew protein database and improve sequence quality for proteins of interest, based on a publicly available cashew genome database. As a result, two additional isoforms for cashew 2S albumins and five other isoforms for cashew 11S proteins were identified, along with several other potential allergens. Using the optimized protein database, the protein profiles of cashew nuts subjected to different oil-roasting conditions (138 °C and 166 °C for 2-10 minutes) were analyzed using discovery LC-MS/MS analysis. The results showed that cashew 2S protein is most heat-stable, followed by 11S and 7S proteins, though protein isoforms might be affected differently. Preliminary target peptide selection indicated that out of the 29 potential targets, 18 peptides were derived from the newly developed database. In the evaluation of thermal processing effects on cashew proteins, several Maillard reaction adducts were also identified. The cashew protein database developed in this study allows for comprehensive analyses of cashew proteome and development of high-quality allergen detection method.
2022-06-07 | PXD027543 | Pride
Project description:In this study, we present a first proteomic overview of macadamia nut using a label-free shotgun proteomic approach and prediction of their proteins with potential allergenic activity and cross-reactivity via an in silico analysis. The defense response proteins were the most abundant group of proteins and accounted for 24% of the total abundance. The vicilin-like macadamia antimicrobial peptides 2-3 (MiAMP2) was the most abundant protein. The cascading of amino acid and carbohydrate metabolic pathways in macadamia nut were constructed and proposed for the first time. The in silico analysis revealed seed storage proteins (conglutins and vicilins), rubber elongation factor proteins, phosphate binding proteins, and detoxifying methylglyoxalases among others as proteins with allergenic and cross-reactive potential. The label-free shotgun proteomics study revealed valuable insight into the genetic and biological makeup of macadamia nut and potential proteins with predictive allergenic activity and cross-reactivity. Integration of genomics with the proteomic data will be indispensable for future molecular characterization of macadamia including allergens.
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Project description:The effect of cashew nut shell liquid on intestinal environment of chicken
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Project description:Cashew is one of the most prevalent causes of tree nut allergies. However, the cashew proteome is far from complete, which limits the quality of peptide identification in mass spectrometric analyses. In this study, bioinformatics tools were utilized to construct a customized cashew protein database and improve sequence quality for proteins of interest, based on a publicly available cashew genome database. As a result, two additional isoforms for cashew 2S albumins and five other isoforms for cashew 11S proteins were identified, along with several other potential allergens. Using the optimized protein database, the protein profiles of cashew nuts subjected to different oil-roasting conditions (138 °C and 166 °C for 2-10 minutes) were analyzed using discovery LC-MS/MS analysis. The results showed that cashew 2S protein is most heat-stable, followed by 11S and 7S proteins, though protein isoforms might be affected differently. Preliminary target peptide selection indicated that out of the 29 potential targets, 18 peptides were derived from the newly developed database. In the evaluation of thermal processing effects on cashew proteins, several Maillard reaction adducts were also identified. The cashew protein database developed in this study allows for comprehensive analyses of cashew proteome and development of high-quality allergen detection method.
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Project description:BRD4-NUT megadomains is an order of magnitude larger than super-enhancer regions and displays a more continuously enriched profile rather than appearing as a cluster of individual peaks. Chip-seq mapping of active chromatin marks in BRD4-NUT and different NMC cells
2015-07-14 | E-GEOD-70870 | biostudies-arrayexpress
Project description:Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma (NC). Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
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Project description:BRD4-NUT and H3K27ac are depleted from megadomains in NUT Carcinoma (NC) cell line TC-797 after treatment with Panobinostat.
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Project description:NUT, nuclear protein in testis is the universal fusion partner of BRD4 in the highly aggressive NUT Midline Carcinoma (NMC), but its physiological function is unknown. Here we show that Nut is exclusively expressed in post-meiotic spermatogenic cells, at the time of genome-wide histone hyperacetylation. Inactivation of Nut induces a spermatogenesis arrest at the histone-to-protamine replacement stage, leading to male infertility. Subsequent molecular investigations show that Nut sustains global histone H4 hyperacetylation in post-meiotic cells. Additionally, Nut mediates a p300/CBP-dependent gene expression program and, by enhancing acetylation of H4 at both K5 and K8 sites, provides binding sites for the first bromodomain of Brdt, which drives histone removal. Our results bring the first evidence of Nut’s function in spermatogenic cells where it uses the ubiquitous HATs p300/CBP to direct a cell-type specific histone H4 hyperacetylation. The ectopic activity of Nut in NMC recreates a forced p300-induced histone hyperacetylation / bromodomain-binding loop that normally operates in post-meiotic spermatogenic cells.
2018-10-15 | GSE111931 | GEO
Project description:Discarded live tumor tissue from a metastatic focus in the patientM-bM-^@M-^Ys lung was collected under institutional review board approval through the NUT midline carcinoma registry (www.NMCRegistry.org). From this tissue the first known NUT-variant cell line, 1221, was established. To determine the putative partner gene to NUT, we performed comprehensive RNA-sequencing on RNA purified from 1221. We identified an in-frame transcript fusing the 5M-bM-^@M-^Y coding sequence of NSD3 (exons 1-7) to exons 2-7 of NUT. Expression of the NSD3-NUT fusion oncoprotein was verified by immunobloting with an antibody to NUT, revealing an approximately 200kDa band that is similar in size to BRD3-NUT, but smaller than BRD4-NUT Identification of a NUT fusion partner using RNA extracted from live cultured 1221 cell line derived from a lung metastasis from the index case of a 13 year old female with NUT-positive NMC.
2014-08-01 | E-GEOD-57222 | biostudies-arrayexpress