| 1. |
- Boccaletto, Pietro, et al.
(författare)
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MODOMICS: a database of RNA modification pathways. 2021 update
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 50:D1, s. D231-D235
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Tidskriftsartikel (refereegranskat)abstract
- The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing and distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. Over the years, prompted by the accumulation of new knowledge and new types of data, it has been updated with new information and functionalities. In this new release, we have created a catalog of RNA modifications linked to human diseases, e.g., due to mutations in genes encoding modification enzymes. MODOMICS has been linked extensively to RCSB Protein Data Bank, and sequences of experimentally determined RNA structures with modified residues have been added. This expansion was accompanied by including nucleotide 5'-monophosphate residues. We redesigned the web interface and upgraded the database backend. In addition, a search engine for chemically similar modified residues has been included that can be queried by SMILES codes or by drawing chemical molecules. Finally, previously available datasets of modified residues, biosynthetic pathways, and RNA-modifying enzymes have been updated. Overall, we provide users with a new, enhanced, and restyled tool for research on RNA modification. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.
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| 2. |
- Destefanis, Eliana, et al.
(författare)
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A mark of disease : How mRNA modifications shape genetic and acquired pathologies
- 2021
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Ingår i: RNA. - : Cold Spring Harbor Laboratory Press (CSHL). - 1355-8382 .- 1469-9001. ; 27:4, s. 367-389
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Forskningsöversikt (refereegranskat)abstract
- RNA modifications have recently emerged as a widespread and complex facet of gene expression regulation. Counting more than 170 distinct chemical modifications with far-reaching implications for RNA fate, they are collectively referred to as the epitranscriptome. These modifications can occur in all RNA species, including messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). In mRNAs the deposition, removal, and recognition of chemical marks by writers, erasers and readers influence their structure, localization, stability, and translation. In turn, this modulates key molecular and cellular processes such as RNA metabolism, cell cycle, apoptosis, and others. Unsurprisingly, given their relevance for cellular and organismal functions, alterations of epitranscriptomic marks have been observed in a broad range of human diseases, including cancer, neurological and metabolic disorders. Here, we will review the major types of mRNA modifications and editing processes in conjunction with the enzymes involved in their metabolism and describe their impact on human diseases. We present the current knowledge in an updated catalog. We will also discuss the emerging evidence on the crosstalk of epitranscriptomic marks and what this interplay could imply for the dynamics of mRNA modifications. Understanding how this complex regulatory layer can affect the course of human pathologies will ultimately lead to its exploitation toward novel epitranscriptomic therapeutic strategies.
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| 3. |
- Shanley, Emer, et al.
(författare)
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Development and psychometric evaluation of the patient knowledge of, and attitudes and behaviours towards pressure ulcer prevention instrument (KPUP).
- 2020
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Ingår i: International Wound Journal. - : Wiley-Blackwell Publishing Inc.. - 1742-4801 .- 1742-481X. ; 17:2, s. 339-350
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Tidskriftsartikel (refereegranskat)abstract
- The Patient Knowledge of, and Attitude and Behaviour towards Pressure Ulcer Prevention Instrument (KPUP) was developed and validated using a two-stage prospective psychometric instrument validation study design. In Stage 1, the instrument was designed, and it is psychometrically evaluated in Stage 2. To establish content validity, two expert panels independently reviewed each item for appropriateness and relevance. Psychometric evaluation included construct validity and stability testing of the instrument. The questionnaire was administered to a convenience sample of 200 people aged more than 65 years, living independently in the community; reliability and stability were assessed by test/retest procedures, with a 1-week interval. Mean knowledge scores at 'test' were 11.54/20 (95% CI = 11.10-11.99, SD: 3.07), and 'retest' was 12.24 (95% CI = 11.81-12.66, SD: 2.93). For knowledge, correlation between the test/retest score was positive (r=. 60), attitude section-inter-item correlations ranged from r = -.31 to r = .57 (mean intraclass correlation coefficient of r = .42), and internal consistency for the retest was the same as the test (α = .41 for the eight items). For health behaviours, individual inter-item correlations for test items ranged from r = -.21 to r = .41 for the 13 standardised items. Psychometric testing of the KPUP in a sample of older persons in the community provided moderate internal consistency and general high test-retest stability.
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