Alternator, Год журнала: 2023, Номер unknown
Опубликована: Окт. 5, 2023
Molecular Aspects of Medicine, Год журнала: 2024, Номер 96, С. 101253 - 101253
Опубликована: Фев. 16, 2024
Massively parallel sequencing technologies have long been used in both basic research and clinical routine. The recent introduction of digital has made previously challenging applications possible by significantly improving sensitivity specificity to now allow detection rare sequence variants, even at single molecule level. Digital utilizes unique molecular identifiers (UMIs) minimize sequencing-induced errors quantification biases. Here, we discuss the principles UMIs how they are sequencing. We outline properties different UMI types consequences various approaches relation experimental protocols bioinformatics. Finally, describe can be applied specific fields, focusing on cancer management where it screening asymptomatic individuals, diagnosis, treatment prediction, prognostication, monitoring efficacy early resistance as well relapse.
Язык: Английский
Процитировано
8
Nature Reviews Molecular Cell Biology, Год журнала: 2024, Номер 25(6), С. 417 - 418
Опубликована: Март 28, 2024
Язык: Английский
Процитировано
6
Zoologica Scripta, Год журнала: 2024, Номер 53(6), С. 754 - 762
Опубликована: Июнь 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.
Язык: Английский
Процитировано
6
Molecular Ecology Resources, Год журнала: 2025, Номер unknown
Опубликована: Янв. 2, 2025
Formalin preservation of museum specimens has long been considered a barrier to molecular research due extensive crosslinking and chemical modification. However, recent optimisation hot alkaline lysis proteinase K digestion DNA extraction methods have enabled growing number studies overcome these challenges conduct genome-wide re-sequencing targeted locus-specific sequencing. The newest, perhaps most unexpected utility formalin in archival samples is its ability preserve situ DNA-protein interactions at level. Retrieving this signal provides information about the relative compaction or accessibility genome transcriptional machinery required for gene expression. Thus, exposure essentially corresponds taking snapshot organism-wide expression time death. While methylation RNA-Seq analyses dried tissues provided glimpses into historical regulation, techniques were previously limited skeletal desiccated remains, offering only partial insights. By examining fluid-preserved specimens, tools can now be applied broader range tissues, enabling more detailed tissue-specific regulation profiling across vertebrates. In review, we chronicle use formaldehyde collections discuss how chromatin with assays like MNase-seq FAIRE-seq are surmounting fixation unlocking invaluable insights genomes profiles. deeper integration genetics bridges gap between past present vital tool that could help us predict mitigate some impacts future environmental change, novel pathogens, invasive species.
Язык: Английский
Процитировано
0
Molecular Ecology, Год журнала: 2023, Номер 32(24), С. 6729 - 6742
Опубликована: Окт. 24, 2023
Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of as experiments has been hampered by limited information on makeup populations that were part earlier invasion stages. Now, developments ancient and historical DNA technologies, well quickening pace digitization millions specimens are housed herbaria museums globally, promise help overcome this obstacle. In review, we first introduce types temporal data can be used invasions, highlighting timescale captured each approach their respective limitations. We then discuss how available from prior studies answer questions mechanisms (mal)adaptation, rates evolution, community-level changes during invasions. By bridging gap between contemporary populations, us connect pattern process science. These will become increasingly important if achieve full potential evolution nature.
Язык: Английский
Процитировано
7
Annals of Botany, Год журнала: 2024, Номер 133(3), С. 459 - 472
Опубликована: Янв. 4, 2024
Abstract Background and Aims Transcriptome sequencing is a cost-effective approach that allows researchers to study broad range of questions. However, preserve RNA for transcriptome sequencing, tissue often kept in special conditions, such as immediate ultracold freezing. Here, we demonstrate can be obtained from 6-month-old, field-collected samples stored silica gel at room temperature. Using these transcriptomes, explore the evolutionary relationships genus Pitcairnia (Bromeliaceae) Dominican Republic infer barriers gene flow. Methods We extracted silica-dried leaf 19 individuals collected across Republic. used series macro- micro-evolutionary approaches examine patterns flow among individuals. Key Results produced high-quality transcriptomes material demonstrated on island match geography more closely than species delimitation methods. A population genetic examination indicates combination ecological geographical features presents Pitcairnia. Conclusions Transcriptomes silica-preserved tissue. The diversity populations does not warrant classification separate species, but contains several flow, notably Cordillera Central mountain range.
Язык: Английский
Процитировано
2
Scientific Reports, Год журнала: 2024, Номер 14(1)
Опубликована: Ноя. 30, 2024
Abstract Natural history museum collections harbour a record of wild species from the past centuries, providing unique opportunity to study animals as well their infectious agents. Thousands great ape specimens are kept in these collections, and could become an important resource for studying evolution DNA viruses. Their genetic material is likely be preserved dry specimens, reported previously monkeypox virus genomes historical orangutan specimens. Here, we screened 209 99 different viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined presence multiple viruses within this dataset obtained several near-complete viral genomes. In particular, report high-coverage (> 18-fold) hepatitis B one gorilla two chimpanzee individuals, which phylogenetically placed clades infecting respective host species.
Язык: Английский
Процитировано
1
Journal of Archaeological Science, Год журнала: 2024, Номер 174, С. 106132 - 106132
Опубликована: Дек. 18, 2024
Язык: Английский
Процитировано
1
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Апрель 28, 2024
Abstract Natural history museum collections harbour a record of wild species from the past centuries, providing unique opportunity to study animals as well their infectious agents. Thousands great ape specimens are kept in these collections, and could become an important resource for studying evolution DNA viruses. Their genetic material is likely be preserved dry specimens, reported previously monkeypox virus genomes historical orangutan specimens. Here, we screened 209 99 different viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined presence multiple viruses within this dataset obtained several near-complete viral genomes. In particular, report high-coverage (>18-fold) hepatitis B one gorilla two chimpanzee individuals, which phylogenetically placed clades infecting respective host species.
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Окт. 3, 2024
ABSTRACT Recovery of virus sequences from old samples provides an opportunity to study evolution and reconstruct historic virus-host interactions. Studies have mainly relied on DNA or RNA fixed frozen samples. The millions specimens in natural history museums represent a potential treasure trove sequences, but it is not clear how well survives We experimentally assessed the stability insects stored dry at room temperature over 72 weeks. Although molecules grew fragmented, yields remained surprisingly constant. RT-qPCR host showed minimal differences between dried specimens. To assess survival much older we acquired Drosophila North American entomological collections. recovered known novel viruses including several coding complete genomes fly collected 1908. found that virome D. melanogaster has changed little past century. Galbut virus, most prevalent infection contemporary , was also common Finally, investigated genomic physical features surviving RNA. survived chemically damaged, preferentially double stranded contained ribonucleoprotein complexes. This - especially certain types – can survive biological extended periods absence fixation freezing confirms utility provide clearer understanding evolution.
Язык: Английский
Процитировано
0