Exploration of the R code-based mathematical model for PMI estimation using profiling of RNA degradation in rat brain tissue at different temperatures

Abstract

Precise estimation of postmortem interval (PMI) is crucial in some criminal cases. This study aims to find some optimal markers for PMI estimation and build a mathematical model that could be used in various temperature conditions. Different mRNA and microRNA markers in rat brain samples were detected using real-time fluorescent quantitative PCR at 12 time points within 144 h postmortem and at temperatures of 4, 15, 25, and 35 °C. Samples from 36 other rats were used to verify the animal mathematical model. Brain-specific mir-9 and mir-125b are effective endogenous control markers that are not affected by PMI up to 144 h postmortem under these temperatures, whereas the commonly used U6 is not a suitable endogenous control in this study. Among all the candidate markers, ΔCt (β-actin) has the best correlation coefficient with PMI and was used to build a new model using R software which can simultaneously manage both PMI and temperature parameters. This animal mathematical model is verified using samples from 36 other rats and shows increased accuracy for higher temperatures and longer PMI. In this study, β-actin was found to be an optimal marker to estimate PMI and some other markers were found to be suitable to act as endogenous controls. Additionally, we have used R code software to build a model of PMI estimation that could be used in various temperature conditions.

Systematic analysis of gene expression patterns associated with postmortem interval in human tissues

“…These results suggested that gene expression changes vary with PMI, and this characteristic might be used to estimate the PMI. Several studies have suggested that mRNA can be used to estimate PMI 3, 9, 19, 31, 32 . Our study thus provides novel direction for selection of the most suitable mRNA indicator for estimating PMI accurately.…”

G6PC3, ALDOA and CS induction accompanies mir-122 down-regulation in the mechanical asphyxia and can serve as hypoxia biomarkers

“…Total RNA was extracted from the samples following the methods described by Ma et al [32]. Briefly, cDNA was generated using a PrimeScript RT Reagent Kit (Takara, Japan) according to the manufacturer's protocol, and 500 ng of total RNA was reverse transcribed by adding a polyA tail using a One-Step Prime-Script miRNA cDNA Synthesis Kit (Takara, Japan) according to the manufacturer's protocol for microRNA analysis.…”

Gene expression in the twilight of death

“…Our experimental design provided "proof of principle" and did not consider factors such as temperature, which have been considered in other PMI models (e.g. [34]). Future studies are needed to incorporate the effects of temperature and the environment on PMI predictions in order to make the design more universal.…”