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Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells.
Front Bioinform
January 2024
Grupo Rnomica Teórica y Computacional, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.
In recent years, a population of small RNA fragments derived from non-coding RNAs (sfd-RNAs) has gained significant interest due to its functional and structural resemblance to miRNAs, adding another level of complexity to our comprehension of small-RNA-mediated gene regulation. Despite this, scientists need more tools to test the differential expression of sfd-RNAs since the current methods to detect miRNAs may not be directly applied to them. The primary reasons are the lack of accurate small RNA and ncRNA annotation, the multi-mapping read (MMR) placement, and the multicopy nature of ncRNAs in the human genome.
View Article and Find Full Text PDFImproved DNA Amplification of the Hallmark IS Element in subsp. : a Reexamination Based on Whole-Genome Sequence Analysis.
Appl Environ Microbiol
February 2023
INRAE, ISP, Université de Tours, Nouzilly, France.
Amplification of the IS multicopy element is a hallmark nucleic acid-based diagnostic test for Mycobacterium avium subsp. , which causes Johne's disease in ruminants. This assay is frequently used to determine the presence of the bacterium in feces of infected cattle and sheep.
View Article and Find Full Text PDFAccessing the Variability of Multicopy Genes in Complex Genomes using Unassembled Next-Generation Sequencing Reads: The Case of Trypanosoma cruzi Multigene Families.
mBio
December 2022
Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Geraisgrid.8430.f, Belo Horizonte, Minas Gerais, Brazil.
Article Synopsis
- Repetitive elements in complex eukaryotic genomes, like that of Trypanosoma cruzi (the Chagas disease parasite), lead to fragmented assembly and underestimate gene variability, particularly in multigene families responsible for host interactions.
- * Our new read-based approach estimates the variability and copy number of key multigene families (MASP, TcMUC, and Trans-Sialidase) across multiple parasite strains, revealing distinct patterns of variation and higher variability in hybrid strains.
- * The findings suggest focusing on TS antigens could enhance diagnosis and vaccine design for Chagas disease, and the methodology is adaptable for studying multicopy genes in other organisms, enabling better insights into complex genomes.
In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue.
Nat Commun
February 2022
MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK.
Mitochondria host key metabolic processes vital for cellular energy provision and are central to cell fate decisions. They are subjected to unique genetic control by both nuclear DNA and their own multi-copy genome - mitochondrial DNA (mtDNA). Mutations in mtDNA often lead to clinically heterogeneous, maternally inherited diseases that display different organ-specific presentation at any stage of life.
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