Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1180220 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31178311_1.fastq.gz | Fastqsanger.gz | |||
| SRR31178311_2.fastq.gz | Fastqsanger.gz | |||
| SRR31178312_1.fastq.gz | Fastqsanger.gz | |||
| SRR31178312_2.fastq.gz | Fastqsanger.gz | |||
| SRR31178313_1.fastq.gz | Fastqsanger.gz |
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Project description:Protein kinases (PKs) are involved in plant growth and stress responses, and constitute one of the largest superfamilies due to numerous gene duplications. However, limited PKs have been functionally described in pecan, an economically important nut tree. Here, the comprehensive identification, annotation and classification of the entire pecan kinome was reported. A total of 967 PK genes were identified from pecan genome, and further classified into 20 different groups and 121 subfamilies using the kinase domain sequences, which were verified by the phylogenetic analysis. The receptor-like kinase (RLK) group contained 565 members, which constituted the largest group. Gene duplication contributed to the expansion of pecan kinome, 169 duplication events including 285 PK genes were found, and Ka/Ks ratio revealed they experienced strong negative selection. GO functional analysis indicated majority PKs involved in molecular functions and biological processes. The RNA-Seq data of PK genes in pecan were further analyzed at subfamily level, and different PK subfamilies performed various expression patterns across different conditions or treatments, suggesting PK genes in pecan involved in multiple biological functions and stress responses. Taken together, this study provided insight into the expansion, evolution and function of pecan PKs. Our findings regarding expansion, expression and co-expression analyses could lay a good foundation for future research to understand the roles of pecan PKs, and find the key candidate genes more efficiently.
2021-07-05 | GSE179336 | GEO
Project description:Background Many environmental and lifestyle factors have been implicated in the decline of sperm quality, with diet being one of the most plausible factors identified in recent years. Moreover, several studies have reported a close association between the alteration of specific sperm DNA methylation signatures and semen quality. Objectives To evaluate the effect of tree nuts consumption on sperm DNA methylation patterns in healthy individuals reporting eating a Western‐style diet. Material and Methods This is a post‐hoc analysis conducted in a subset of participants (healthy, non‐smoking, and young) from the FERTINUTS 14‐wk randomized‐controlled, parallel‐trial, recruited between December 2015 and February 2017. The participants included in the current study (n=72) were randomly selected in a proportion 2:1 from the original FERTINUTS trial between the 98 participants that completed the entire dietary intervention (nut group, n=48; control group, n=24). Sperm DNA methylation patterns were examined at baseline and after 14 weeks in 48 individuals consuming 60 g/d of mixed nuts (nuts group) and in 24 individuals following the usual Western‐style diet avoiding consumption of nuts (control group). Results Over the course of the trial, no significant changes in global methylation were observed between groups. However, in the nuts group, we identified 36 genomic regions that were significantly differentially methylated between the baseline and the end of the trial and 97.2% of the regions displayed hypermethylation. We identified no such change in the control group over the same period of time. We also utilized the recently developed germ line age calculator to determine if nut consumption resulted in alterations to the epigenetic age of cells and no significant differences were found. Discussion and Conclusion Adding nuts to a regular Western‐style diet subtly impacts sperm DNA methylation in specific regions, demonstrating that there are some sperm epigenome regions that could respond to diet.
2020-09-24 | GSE140004 | GEO
Project description:Interventions: Participants will take 6 brazil nuts a day for four weeks.
This four week intervention will be preceded by a 4 week run-in / wash out phase
participants will be advised to exclude any selenium rich foods or green tea during the study
This Pilot study will confirm the amount of Brazil Nuts we will use in the study comparing with green tea. This follow up study (Effects of combining Selenium (Se) and green tea on biomarkers for colorectal cancer prevention in human subjects). will be registered with ANZCTR in the near future’
At the initial interview dietary advice will be given. This will give an understanding of the nature of the volunteers diet and the likely influence of Se to the diet and suitability to become involved in the study
(if intolerant to nuts volunteers will not participate in the study)
We will ask participants not to consume, whenever possible, throughout the study:-
Any selenium supplement
Any selenium enriched foods, such as nuts, sea food (such as tuna or octopus)
The Brazil nut is a large nut that comes from the castanheiro de para tree in Brazil’s rainforests. Each serving of about six to eight nuts contains 4 g of protein and 7 grams each of monosaturated and polysaturated fat.
Brazil nuts (Berholletia excelas, family Lecythidaceae) are the richest known food source of selenium, with mean concentrations reported in the literature between 8-83 micrograms Se/g
6 Brazil nuts daily provides 48 micrograms Se/day - 53 micrograms Se/day
Primary outcome(s): If supplementation of 6 Brazil nuts/day increases plasma Selenium (Se) levels
A blood sample (5mls of whole blood taken on 2 occasions) will be collected at baseline and after intervention, testing for plasma Selenium levels[Blood samples collected at commencement of intervention (week 0) and at end of intervention (wk 4)]
Study Design: Purpose: Prevention; Allocation: Non-randomised trial; Masking: Open (masking not used);Assignment: Single group;Type of endpoint: Safety
| 2458510 | ecrin-mdr-crc
Project description:Areca nut(Areca catechu L.) is commonly consumed as a chewing food in the Asian region. However, the investigations into the components of areca nut are limited. In this study, we have developed an approach that combines mass spectrometry with feature-based molecular network to explore the chemical characteristics of the areca nut. In comparison to the conventional method, this technique demonstrates a superior capability in annotating unknown compounds present in areca nut. We annotated a total of 52 compounds, including one potential previously unreported alkaloids, one carbohydrate, and one phenol and confirmed the presence of 6 of them by comparing with commercial standards. The validated method was used to evaluate chemical features of areca nut at different growth stages, annotating 25 compounds as potential biomarkers for distinguishing areca nut growth stages. Therefore, this approach offers a rapid and accurate method for the component analysis of areca nut.
2023-11-10 | MSV000093351 | MassIVE
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:To determine mechanisms of synergy between EZH2 and BRD4-NUT, we treated NUT carcinoma cell lines with EZH2 inhibitor, tazemetostat, and/or BET bromodomain inhibitors (ABBV075 pan-BET inhibitor or ABBV744 BD2-selective inhibitor). We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different NUT carcinoma cell lines at two time points, 6h and 96h.
2023-10-05 | GSE208774 | GEO
Project description:Interventions: 30 healthy volunteers (>50yrs) at-risk for CRC by virtue of age and /or other standard risk factors will be recruited to participate in a randomised, three cohort dietary intervention study. with a parallel design to test the effects of Se and green tea alone and in combination on molecular biomarkers for CRC prevention in the normal rectal epithelial cells. They will be instructed to maintain their usual diet during the study but to avoid supplementation with any green tea-related food or drink (limited to <3 cups of black tea per day), and Se-rich foods such as octopus, crab and tuna, liver and kidney or additional Brazil nuts or other nuts (except those Brazil nuts and green tea extract prescribed by us). The study will consist of dietary intervention period of 6 weeks, preceded by a run in period of 4 weeks.
The volunteers will be randomised (randomisation will be computer generated) into one of three groups of 10, receiving
1) Se, supplied as Brazil nuts (6 Brazil nuts daily will provide 48micrograms Se/day);
2) Green tea, supplied as a green tea extract capsule (4 capsules daily will provide 800mg EGCG/day); and
3) Se + green tea (6 Brazil nuts daily + 4 green tea extract capsules daily (will provide 48micrograms Se/day and 800mg EGCG/day).
Six Brazil nuts has been chosen because the average Se concentration (2.7 micrograms Se/g) in Brazil nuts (supplied from Charlesworth, Australia) is relatively low compared to that of the report by Thomson et al, where the Se concentration is 6.4micrograms Se/g, and average weight for one nut is 4g, 2 nuts provided 53 micrograms Se/day (Am J Clin Nutr 2008;87:379-3840). Since the average weight of one Brazil nut (supplied from Charlesworth, Australia) is 3g, 6 Brazil nuts daily will provide 48microgra
Primary outcome(s): Effects of combination diet (Se + green tea) on biomarkers of Wnt pathway (catenin), inflammation (COX-2) and DNA repair (MGMT) in rectal epithelium. Rectal biopsies will be collected and examined by RT-PCR and immunohistochemistry for the expression of these biomarkers at gene and protein levels[Commencement of Intervention (Baseline),
End of intervention (6 weeks) ]
Study Design: Purpose: Prevention; Allocation: Randomised controlled trial; Masking: Open (masking not used);Assignment: Parallel;Type of endpoint: Efficacy
| 2459098 | ecrin-mdr-crc