Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life DOI Creative Commons
Alexa S. Tyszka, Drew A. Larson, Joseph F. Walker

et al.

Trends in Plant Science, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Language: Английский

A renaissance of microRNAs as taxonomic and phylogenetic markers in animals DOI Creative Commons
Bastian Fromm

Zoologica Scripta, Journal Year: 2024, Volume and Issue: 53(6), P. 754 - 762

Published: June 21, 2024

Abstract Molecular markers for tracing animal sample origins and compositions are critical applications such as parasite detection, contamination screening, authentication. Among these, microRNAs have emerged promising candidates due to their deep conservation, near‐hierarchical evolution, stability. I here review the suitability of taxonomic also phylogenetic show how careful annotation efforts establishment curated microRNA gene database MirGeneDB tools like MirMachine revitalized research. These advancements enable accurate studies, highlighting microRNAs' potential in resolving long‐standing questions relationships extending ancient DNA environmental RNA analysis. Future research must focus on expanding complements across all Metazoa further improving methodologies.

Language: Английский

Citations

6
Assessing Transcriptomic Signatures of Aging: Testing an mRNA Marker Panel for Forensic Age Estimation of Blood Samples DOI Creative Commons
Nadescha Viviane Hänggi, Jacqueline Neubauer,

Yael Marti

et al.

Forensic Science International Genetics, Journal Year: 2025, Volume and Issue: unknown, P. 103282 - 103282

Published: April 1, 2025

Estimating the age of an unknown perpetrator can be a valuable tool in narrowing down group suspects. Research efforts to estimate stain donor have mainly focused on epigenetic modifications, but there is evidence that RNA expression patterns, i.e. composition transcriptome, change with increasing age, which could promising molecular alternative for prediction. In previous study, we identified total 508 mRNA markers related from two blood whole transcriptome sequencing data sets, using differential analysis DESeq2 and marker selection lasso regression. For this selected both approaches were combined into RNA-specific targeted MPS assay Ion Torrent platform evaluated 100 EDTA samples healthy donors (aged between 23 73 years). We compared three different normalization methods obtained investigated performance various regression techniques The model based elastic net dSVA-normalized exhibited most robust performance, achieving MAE 9.29 years correlation 0.57 chronological predicted age. Although use approach instead RNA-Seq offers several advantages forensic setting, observed considerable amount unwanted variation data. conclude it challenging detect distinct signals associated

Language: Английский

Citations

0
Identification of individuals from low template blood samples using whole transcriptome shotgun sequencing DOI Creative Commons

Alberte Honoré Jepsen,

Marie-Louise Kampmann,

Stine Bøttcher Jacobsen

et al.

Forensic Science International Genetics, Journal Year: 2024, Volume and Issue: 72, P. 103089 - 103089

Published: June 19, 2024

Language: Английский

Citations

2
The sedaDNA revolution and archaeology: Progress, challenges, and a research agenda DOI Creative Commons
Antony G. Brown,

M. I. Lucas,

Inger Greve Alsos

et al.

Journal of Archaeological Science, Journal Year: 2024, Volume and Issue: 174, P. 106132 - 106132

Published: Dec. 18, 2024

Language: Английский

Citations

1
Ancient environmental microbiomes and the cryosphere DOI Creative Commons
Alexander D. Williams, Vivian Leung, Julian W. Tang

et al.

Trends in Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges opportunities for studying ancient environmental microbiomes (AEMs). a field currently reliant on several assumptions, discuss theoretical empirical feasibility recovering microbial nucleic acids (NAs) from permafrost varying degrees antiquity. We also summarize contamination control best practices highlight considerations latest approaches, including shotgun metagenomics, downstream bioinformatic authentication approaches. review adoption existing software provide an overview more recently published programs, reference to their suitability AEM studies. Finally, outstanding likely future directions research.

Language: Английский

Citations

0
Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life DOI Creative Commons
Alexa S. Tyszka, Drew A. Larson, Joseph F. Walker

et al.

Trends in Plant Science, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Language: Английский

Citations

0