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Basic Science and Pathogenesis.
Alzheimers Dement
December 2024
The University of Arizona - Tucson, Tucson, AZ, USA.
Background: Host commensal gut microbes are shown to be crucial for microglial maturation, and functions that involve innate immune responses to maintain brain homeostasis. Sex has a crucial role in the incidence of neurological diseases with females showing higher progression of AD compared with males. Transcriptomics has been a powerful tool for the characterization of microglial phenotypes however, there is a large gap in relating to their functional protein abundances.
View Article and Find Full Text PDFBayesAge 2.0: a maximum likelihood algorithm to predict transcriptomic age.
Geroscience
January 2025
Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
Aging is a complex biological process influenced by various factors, including genetic and environmental influences. In this study, we present BayesAge 2.0, an upgraded version of our maximum likelihood algorithm designed for predicting transcriptomic age (tAge) from RNA-seq data.
View Article and Find Full Text PDFReframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies.
Mol Ecol Resour
January 2025
National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, Australian Capital Territory, Australia.
Formalin preservation of museum specimens has long been considered a barrier to molecular research due to extensive crosslinking and chemical modification. However, recent optimisation of hot alkaline lysis and proteinase K digestion DNA extraction methods have enabled a growing number of studies to overcome these challenges and conduct genome-wide re-sequencing and targeted locus-specific sequencing. The newest, and perhaps most unexpected utility of formalin preservation in archival samples is its ability to preserve in situ DNA-protein interactions at a molecular level.
View Article and Find Full Text PDFPolygenic score distribution differences across European ancestry populations: implications for breast cancer risk prediction.
Breast Cancer Res
December 2024
Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus.
Background: The 313-variant polygenic risk score (PRS) provides a promising tool for clinical breast cancer risk prediction. However, evaluation of the PRS across different European populations which could influence risk estimation has not been performed.
Methods: We explored the distribution of PRS across European populations using genotype data from 94,072 females without breast cancer diagnosis, of European-ancestry from 21 countries participating in the Breast Cancer Association Consortium (BCAC) and 223,316 females without breast cancer diagnosis from the UK Biobank.
Cytidine analogs in plant epigenetic research and beyond.
J Exp Bot
December 2024
Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Acad Sci, Šlechtitelů 31, Olomouc 77900, Czech Republic.
Cytosine (DNA) methylation plays important roles in silencing transposable elements, plant development, genomic imprinting, stress responses, and maintenance of genome stability. To better understand the functions of this epigenetic modification, several tools have been developed to manipulate DNA methylation levels. These include mutants of DNA methylation writers and readers, targeted manipulation of locus-specific methylation, and the use of chemical inhibitors.
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