Ontology highlight
ABSTRACT:
PROVIDER: PRJNA810772 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18156153_1.fastq.gz | Fastqsanger.gz | |||
| SRR18156153_2.fastq.gz | Fastqsanger.gz |
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Project description:Post-mating responses play a vital role in successful reproduction across diverse species. In fruit flies, sex peptide (SP) binds to sex peptide receptor (SPR), triggering a series of post-mating responses. However, the origin of SPR predates the emergence of SP. The evolutionary origins of the interactions between SP and SPR and the mechanisms by which they interact remain enigmatic. In this study, we used ancestral sequence reconstruction, AlphaFold2 predictions, and molecular dynamics simulations to study SP-SPR interactions and their origination. Using AlphaFold2 and long-time molecular dynamics (MD) simulations, we demonstrate the structure and dynamics of SP-SPR interactions. We show that SP potentially binds to the ancestral states of Diptera SPR. Notably, we found that only a few amino acid changes in SPR are sufficient for the formation of SP-SPR interactions. Ancestral sequence reconstruction and MD simulations further reveal that SP-SPR interacts through residues that are mostly located at the SPR interface of an ancestral ligand, myoinhibitory peptides (MIPs). We propose a potential mechanism whereby SP-SPR interactions arise from pre-existing MIP-SPR interface as well as early chance events that created novel SP-specific SP-SPR interactions. Our findings provide new insights into the origin and evolution of SP-SPR interactions and their relationship with MIP-SPR interactions.
2024-03-20 | PXD044633 | Pride
Project description:To study whether there are differences in chromatin-mediated regulation between and within chromosomes in Fusarium oxysporum f. sp. lycopersici 4287 (FGSC9935), we determined the distribution of histone marks associated with euchromatin (H3K4me2) and facultative heterochromatin (H3K27me3) in vitro. We then determined whether these differences correlate with differences in dispensability and sequence divergence and gene expression.
2018-10-16 | GSE121283 | GEO
Project description:The seminal plasma (sp), especially the extracellular vesicles of seminal plasma (sEV) which change with age can affect the endometrial immune microenvironment of female mice. However, it is unclear whether the decline in fertility of reproductively old males is related to the alterations of the sp and sEV which may have compromised effect on the immune microenvironment of the female uterus. In this research, we found a decrease in the implantation rate of pseudo-pregnant female mice which was treated with sp from reproductively old male mice (aged-sp group) than sp from young male mice (young-sp group). RNA-sequence analysis revealed an increase in the expression level of local cytokines and chemokines in the uterus of aged-sp groups than those of young-sp groups. Further in vitro experiments found an induction of dendritic cells (DC) maturation in the aged-sp groups. After isolating and characterizing sEV in young and aged male mice, we perfused the uterus of aged-sp group with sEV from young male mice and found it could partially rescue the low implantation rate of the aged-sp group. Further in vitro experiments found an induction of DC maturation after treating with sEV from aged male mice than that from young male mice, which indicated an age-related activation effect of sp and sEV. In conclusion, we found sp and sEV from aged male mice could induce the maturation of DC, which compromised the microenvironment of female reproductive tract, therefore leading to a decrease in implantation rate.
2021-07-27 | GSE180444 | GEO
Project description:BACKGROUND: Human SP-A1 and SP-A2, encoded by SFTPA1 and SFTPA2 and their genetic variants differentially impact alveolar macrophage (AM) functions and regulation, including the miRNome. We investigated whether miRNome differences previously observed between AM from SP-A2 and SP-A1/SP-A2 mice are due to continued qualitative differences or a delayed response of mice carrying a single gene. METHODS: Human transgenic (hTG) mice, carrying SP-A2 or both SP-A genes and SP-A-KO mice were exposed to filtered air (FA) or O3. AM miRNA levels, target gene expression and pathways determined 18 h after O3 exposure. RESULTS: We found: (a) Differences in miRNome due to sex, SP-A genotype, and exposure; (b) miRNome of both sexes was largely downregulated by O3 ; co-ex had fewer changed (≥2X) miRNAs than either group. (c) the number and direction of expression of genes with significant changes in males and females in co-ex is almost the opposite of those in SP-A2; (iv) The same pathways were found in the studied groups; (e) O3 exposure attenuated sex differences; a higher number of genotype-dependent and genotype-independent miRNAs was common in both sexes after O3 exposure. CONCLUSION: Qualitative differences between SP-A2 and co-ex persist 18 h post-O3, and O3 attenuates sex differences.
2021-01-06 | GSE158401 | GEO
Project description:Human SP-A1 and SP-A2, encoded by SFTPA1 and SFTPA2 and their genetic variants differentially impact alveolar macrophage (AM) functions and regulation, including the miRNome. single dose of SP-A exogenous treatment of SP-A-KO mice prior to infection, after infection, or at the time of infection significantly improved survival. we investigated the role of exogenous SP-A protein treatment on the regulation of AM miRNome in SP-A-KO mice at the time of infection. Towards this, SP-A-KO male and female mice were infected with K. pneumoniae alone or in combination with exogenous SP-A2 (1A0) protein for 6 h, and the expression levels of AM miRNAs, target mRNAs of the significant miRNAs, and pathways involved were studied. We found (i) significant differences in AM miRNome of KO in terms of sex and exposure; (ii) the expression of the overwhelming majority of miRNA targets in KO males were increased in response to infection and exogenous SP-A2 (1A0) protein treatment at the time of infection; (iii) miRNA-mRNA targets were involved in the pro-inflammatory response, anti-apoptosis, cell cycle, cellular growth and proliferation pathways. These data may assist in studying molecular mechanisms of exogenous SP-A mediated the AM miRNome regulation and potentially identify novel therapeutic targets for K. pneumoniae infection.
2023-04-21 | GSE173157 | GEO
Project description:In humans there are two surfactant protein A (SP-A) functional genes SFTPA1 and SFTPA2 encoding innate immune molecules, SP-A1 and SP-A2, respectively, with numerous genetic variants each. SP-A interacts and regulates many of the functions of alveolar macrophages (AM). It is shown that SP-A variants differ in their ability to regulate the AM miRNome in response to oxidative stress (OxS). Because humans have both SP-A gene products, we were interested to determine the combined effect of co-expressed SP-A1/SP-A2 (co-ex) in response to ozone (O3) induced OxS on AM miRNome. Human transgenic (hTG) mice, carrying both SP-A1/SP-A2 (6A2/1A0, co-ex) and SP-A- KO were utilized. The hTG and KO mice were exposed to filtered air (FA) or O3 and miRNA levels were measured after AM isolation with or without normalization to KO. We found: (i) The AM miRNome of co-ex males and females in response to OxS to be largely downregulated after normalization to KO, but after Bonferroni multiple comparison analysis only in females the AM miRNome remained significantly different compared to control (FA); (ii) The targets of the significantly changed miRNAs were downregulated in females and upregulated in males; (iii) Several of the validated mRNA targets were involved in pro-inflammatory response, anti-apoptosis, cell cycle, cellular growth and proliferation; (iv) The AM of SP-A2 male, shown, previously to have major effect on the male AM miRNome in response to OxS, shared similarities with the co-ex, namely in pathways involved in the pro-inflammatory response and anti-apoptosis but also exhibited differences with the cell-cycle, growth, and proliferation pathway being involved in co-ex and ROS homeostasis in SP-A2 male. We speculate that the presence of both gene products versus single gene products differentially impact the AM responses in males and females in response to OxS.
2019-08-02 | GSE135233 | GEO
Project description:To better understand the molecular mechanisms of SP cells, we screened the miRNAs expression patterns in the SP compared with the MP cells. MiRCURY™ LNA array analysis of sorted SP and MP cells from two relapsed myeloma patients with more than 70% bone marrow plasma cells were performed.
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Project description:ATAC-seq in DN, DP, CD4 SP and CD8 SP thymocytes isolated from 9 weeks-old wild type C57BL/6J mouse
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