Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

Kagzi, Kaushar; Hechler, Robert; Fussman, Gregor F; Cristescu, Melania E.

doi:10.22541/au.164580004.43494403/v1

Cited by 7 publications

(12 citation statements)

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“…An inverse-urnshaped pattern of the impact of pH on DNA degradation was noted for 24, 48, and 72 hours respectively. The obtained results were found to be in line with the other previously reported literature studies (Kagzi et al, 2022).…”

Section: Resultssupporting

confidence: 93%

“…Intrinsic variables include, among other things, body mass and surface area, but also age, sex, ante mortem medical problems, the presence of injuries/trauma, the amount of bacterial activity, and the cause of death. A thorough understanding of the susceptibility of post-mortem changes to such factors is critical because these are likely to affect both the appearance of the changes as well as the rate of decay, thus either speeding up or slowing down the progression of post-mortem events (Hau et al, 2014;Kagzi et al, 2022). This is undoubtedly one of the most important reasons why estimating the PMI has remained a difficult problem in forensic science for hundreds of years.…”

Section: Introductionmentioning

confidence: 99%

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An optimization-based study of the impact of different parameters on dna degradation

Bashar

Bardhan²,

Paul³

2022

IJERR

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Human remains exposed to various conditions throughout time are frequently utilized for DNA analysis of tissue or bone for identification reasons. The deterioration and loss of DNA in particular environmental settings have previously created a dilemma for investigators. The post-mortem interval (PMI) or time since death is sometimes the most sought-after piece of information in a medical death investigation. Based on the discovery that DNA degradation has a disproportionate effect on the analysis of bigger genetic loci in particular studies, it was postulated that DNA degradation as a result of autolysis or putrefaction might be useful as a possible rate-of-change indicator of PMI. As a sample, goat liver tissue was used. It was incubated in three testing factors, namely pH, salt content, and sugar concentration, and was compared to a control sample that had not been incubated in any of these parameters. The samples were incubated for 24, 48, and 72 hours. An appropriate Lysis Buffer was used to isolate the DNA. Following the isolation of the DNA, quantitative analysis was performed in a UV-Visible Spectrophotometer (for both the control and incubated samples), followed by Agarose Gel Electrophoresis. It was discovered that the data provided by these studies, taken as a whole, show that we can give information relevant for calculating the post-mortem interval, mostly within the first 72 hours following death. Later, it was decided to use Response Surface Methodology (RSM) to optimize the parameters we had picked, with the BBD design model being the favoured choice. This was done with the help of software named, Design-Expert v11. A Fit Summary that showed a linear model fit for the data. ANOVA was used to generate an equation that may be used to quantify the amount of DNA present in a tissue sample that has been exposed to a specific value of pH, salt concentration, and sugar concentration. Finally, a 3-D response surface curve was produced, two factors at a time, to highlight the variance in DNA loss when those two parameters are taken into account.

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Section: Resultssupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

An optimization-based study of the impact of different parameters on dna degradation

Bashar

Bardhan²,

Paul³

2022

IJERR

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“…Most RNA molecules are only transcribed, and therefore present, in certain cell types and at certain times, so they may carry functional information about the physiological conditions of the host organism (Veilleux et al, 2021). As RNA is less stable than DNA, eRNA degrades more rapidly than eDNA does and so persists for a shorter time in the environment (Kagzi et al, 2022). For example, a study showed that eRNA in water from two marine invertebrates became undetectable after 13 h, compared to 94 h for eDNA from the same samples (Wood et al, 2020).…”

Section: New Frontiers In Fish Edna Researchmentioning

confidence: 99%

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

et al. 2022

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Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods.Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and costeffective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

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“…False discovery rate is defined as the number of false positives as a proportion of the sum of true positives and false positives. Some studies have proposed that eRNA might detect cellularly active taxa only, as opposed to dead and dormant taxa or resuspended sedimentary DNA, and thus minimize the false discovery rate when compared with eDNA (Dowle et al, 2015; Pawlowski et al, 2014; Pochon et al, 2017; Visco et al, 2015, although see Brandt et al, 2020); to date laboratory degradation experiments have found mixed results on whether eRNA degrades faster than eDNA (Kagzi et al, 2022; Wood et al, 2020). Further studies in a field setting will be needed to determine the advantages of eRNA of overcoming false positives detected by eDNA sampling, should they exist.…”

Section: Discussionmentioning

confidence: 99%

“…There was no significant difference in the false discovery rate between eDNA and eRNA. False discovery rate is defined as the num- Pochon et al, 2017;Visco et al, 2015, although see Brandt et al, 2020); to date laboratory degradation experiments have found mixed results on whether eRNA degrades faster than eDNA (Kagzi et al, 2022;Wood et al, 2020). Further studies in a field setting will be needed to determine the advantages of eRNA of overcoming false positives detected by eDNA sampling, should they exist.…”

Section: Discussionmentioning

confidence: 99%

Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA

Littlefair

Rennie

Cristescu

2022

Molecular Ecology Resources

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Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received much attention, the potential of environmental RNA as a biomonitoring tool remains under‐explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect “metabolically active” parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra‐organismal RNA will be important, but viability needs to be examined in a field‐based setting. In this study we evaluate (a) whether extra‐organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools.

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Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

Cited by 7 publications

References 0 publications

An optimization-based study of the impact of different parameters on dna degradation

An optimization-based study of the impact of different parameters on dna degradation

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA

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