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This is currently explored using peptides generated from tardigrade sequences in cell culture.
Cellular and developmental process gene ontologies were overrepresented among the differentially regulated genes, whereas sequences in cell death and immune response categories were underrepresented.
Positioned CENP-A nucleosomes were reported in human neocentromeres on nonrepetitive sequences in cell lines derived from three individuals (Hasson et al. 2013), indicating that nucleosome positions can be stably inherited in these centromeres.
Another explanation for the discussed discrepancies may be the more thorough genetic analysis of TP53 gene sequences in cell lines compared to tumour samples, which implies that cell line studies are more reliable in this respect.
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Methylation patterns of all these sequences in cells expressing GFP-Dnmt1ΔCXXC were very similar to those in GFP-Dnmt1 expressing cells, including the lack of (re-) methylation at the H19a promoter.
Furthermore, the same group detected these hypomethylated DNA sequences in cell-free DNA extracted from maternal plasma during pregnancy, indicating the presence of cffDNA in the maternal circulation.
Whether novel sequences in cells could arise from spontaneous point mutation remains an open question.
However, when ligated plasmids were sequenced, there were significantly higher joining errors with mutated sequences in cells with p53 knockdown compared to the control (9% vs. 3%, p < 0.05; Fig. 5C).
In both cases, little or no amplification product was observed when using synergid cell DNA, indicating reduced methylation of the endogenous and transgenic CRP4 coding sequences in cells where the CRP4 promoter is active.
Chromatin immunoprecipitation (ChIP) experiments performed with antibodies specific for H3K9Ac revealed that H3K9Ac levels are elevated on subtelomeric sequences in cells lacking sir2, and that the sir2N247A mutant causes the same enrichment of H3K9Ac as does loss of sir2.
The differential anchorage-independent growth phenotypes of H1299 cells expressing either IRP2Δ73 or IRP2wt (Fig. S1) also imply a functional significance of this sequence in cell proliferation.
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