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Improved DNA Extraction from Sediments using Modified Ancient DNA Techniques

https://doi.org/10.2139/ssrn.5817232
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Erosion regime controls sediment environmental DNA ‐based community reconstruction
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Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities
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Permafrost microbial communities follow shifts in vegetation, soils, and megafauna extinctions in Late Pleistocene NW North America
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Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA
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Anthropogenic Sediments and Soils: Geoarchaeology
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Ancient DNA Extraction from Soils and Sediments
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Recovery of bulk DNA from soil by a rapid, small-scale extraction method
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Sedimentary DNA for tracking the long-term changes in biodiversity
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The extraction and purification of microbial DNA from sediments
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Quantification and analysis of nucleic acids
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Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments
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Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment
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Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments
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Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites
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Moisture can be the dominant environmental parameter governing cadaver decomposition in soil
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Forensic implications of genetic analyses from degraded DNA—A review
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Amplification and sequencing of Trichuris trichiura ancient DNA extracted from archaeological sediments
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Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics
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Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes
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Pre-industrial cyanobacterial dominance in Lake Moon (NE China) revealed by sedimentary ancient DNA
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Sedimentary ancient DNA sequences reveal marine ecosystem shifts and indicator taxa for glacial-interglacial sea ice conditions
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The persistence of human DNA in soil following surface decomposition
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Novel perspectives to purify genomic DNA from high humic acid content and contaminated soils
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Cycling of extracellular DNA in the soil environment
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Binding of DNA on humic acids: Effect on transformation of Bacillus subtilis and resistance to DNase
inferredcites →https://doi.org/10.1017/qua.2020.59openalex-snapshot
Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set
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Comparative assessment of DNA extraction procedures forAscarisspp. eggs
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Analyzing real-time PCR data by the comparative CT method
inferredcites →https://doi.org/10.1038/s41467-021-27439-6openalex-snapshot
Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA
inferredcites →https://doi.org/10.1038/s41586-021-03675-0openalex-snapshot
Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave
inferredcites →https://doi.org/10.1038/s41598-021-82578-6openalex-snapshot
Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes
inferredcites →https://doi.org/10.1038/s43017-021-00158-8openalex-snapshot
Sedimentary ancient DNA as a tool in paleoecology
inferredcites →https://doi.org/10.1038/s43586-020-00011-0openalex-snapshot
Ancient DNA analysis
inferredcites →https://doi.org/10.1071/mf19175openalex-snapshot
A muddy time capsule: using sediment environmental DNA for the long-term monitoring of coastal vegetated ecosystems
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Late Pleistocene Faunal Assemblages from Karst Cave Settings on Northern Vancouver Island, Canada
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Inclusion of polyvinylpyrrolidone in the polymerase chain reaction reverses the inhibitory effects of polyphenolic contamination of RNA
inferredcites →https://doi.org/10.1098/rstb.2013.0383openalex-snapshot
Ancient and modern environmental DNA
inferredcites →https://doi.org/10.1099/acmi.0.000868.v3openalex-snapshot
Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing
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Assessing the Utility of Soil DNA Extraction Kits for Increasing DNA Yields and Eliminating PCR Inhibitors from Buried Skeletal Remains
inferredcites →https://doi.org/10.1111/1755-0998.12470openalex-snapshot
Comparing the performance of three ancient DNA extraction methods for high‐throughput sequencing
inferredcites →https://doi.org/10.1111/1755-0998.13162openalex-snapshot
An optimized method for the extraction of ancient eukaryote DNA from marine sediments
inferredcites →https://doi.org/10.1111/1755-0998.13903openalex-snapshot
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community
inferredcites →https://doi.org/10.1111/j.1365-2672.2012.05384.xopenalex-snapshot
PCR inhibitors - occurrence, properties and removal
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05261.xopenalex-snapshot
Meta‐barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05470.xopenalex-snapshot
Towards next‐generation biodiversity assessment using DNA metabarcoding
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05545.xopenalex-snapshot
DNA from soil mirrors plant taxonomic and growth form diversity
inferredcites →https://doi.org/10.1126/science.1084114openalex-snapshot
Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments
inferredcites →https://doi.org/10.1126/science.aam9695openalex-snapshot
Neandertal and Denisovan DNA from Pleistocene sediments
inferredcites →https://doi.org/10.1126/science.abf1667openalex-snapshot
Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments
inferredcites →https://doi.org/10.1128/aem.00019-16openalex-snapshot
Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed
inferredcites →https://doi.org/10.1128/aem.02161-07openalex-snapshot
Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics
inferredcites →https://doi.org/10.1128/aem.54.12.2908-2915.1988openalex-snapshot
Recovery of DNA from soils and sediments
inferredcites →https://doi.org/10.1128/aem.58.7.2292-2295.1992openalex-snapshot
Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction
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Development and Application of a New Method To Extract Bacterial DNA from Soil Based on Separation of Bacteria from Soil with Cation-Exchange Resin
inferredcites →https://doi.org/10.1128/aem.58.9.2717-2722.1992openalex-snapshot
Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction
inferredcites →https://doi.org/10.1139/w11-049openalex-snapshot
Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils
inferredcites →https://doi.org/10.1146/annurev.anthro.29.1.217openalex-snapshot
Ancient DNA Studies in Physical Anthropology
inferredcites →https://doi.org/10.1177/0959683615612563openalex-snapshot
Sedimentary ancient DNA from Lake Skartjørna, Svalbard: Assessing the resilience of arctic flora to Holocene climate change
inferredcites →https://doi.org/10.1186/1475-2891-9-23openalex-snapshot
Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens
inferredcites →https://doi.org/10.1251/bpo6openalex-snapshot
Methods for microbial DNA extraction from soil for PCR amplification
inferredcites →https://doi.org/10.1353/hub.2003.0050openalex-snapshot
Hypersensitive PCR, Ancient Human mtDNA, and Contamination
inferredcites →https://doi.org/10.1371/journal.pntd.0013135openalex-snapshot
Sedimentary ancient DNA as part of a multimethod paleoparasitology approach reveals temporal trends in human parasitic burden in the Roman period
inferredcites →https://doi.org/10.1371/journal.pone.0129102openalex-snapshot
Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone
inferredcites →https://doi.org/10.1385/abab:134:2:97openalex-snapshot
Comparative Study of Methods for Extraction and Purification of Environmental DNA From Soil and Sludge Samples
inferredcites →https://doi.org/10.14295/cs.v9i2.2734openalex-snapshot
Spectroscopic and elementary characterization of humic substances in organic substrates
inferredcites →https://doi.org/10.2144/btn-2022-0032openalex-snapshot
A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities
inferredcites →https://doi.org/10.2174/1874940201003010038openalex-snapshot
Assessing PCR Inhibition from Humic Substances
inferredcites →https://doi.org/10.3389/fevo.2019.00189openalex-snapshot
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
inferredcites →https://doi.org/10.3390/analytica3030025openalex-snapshot
Performance of Spectrophotometric and Fluorometric DNA Quantification Methods
inferredcites →https://doi.org/10.3390/microorganisms9040719openalex-snapshot
Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia)
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The effects of humic substances on DNA isolation from soils
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