An optimization-based study of the impact of different parameters on DNA degradation
Abstract
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.
References
Beena, V. (2019). Applications of livestock in biomedical research. J. Dairy Vet. Anim. Res. 8: 107-109.
Creighton, G., Oliffe, J. L., Butterwick, S., & Saewyc, E. (2013). After the death of a friend: Young men's grief and masculine identities. Social Science & Medicine. 84: 35-43.
Gaur, P. K., Mishra, S., Kumar, A., & Panda, B. P. (2014). Development and optimization of gastroretentive mucoadhesive microspheres of gabapentin by Box–Behnken design. Artificial cells, Nanomedicine and Biotechnology. 42(3): 167-177.
Hau, T. C., Hamzah, N. H., Lian, H. H., & Hamzah, S. P. A. A. (2014). Decomposition process and post-mortem changes. Sains Malaysiana. 43(12):1873-1882.
Jatlow, P. I., Agro, A., Wu, R., Nadim, H., Toll, B. A., Ralevski, E., & O'Malley, S. S. (2014). Ethyl glucuronide and ethyl sulfate assays in clinical trials, interpretation, and limitations: results of a dose ranging alcohol challenge study and 2 clinical trials. Alcoholism: Clinical and Experimental Research. 38(7): 2056-2065.
Kagzi, K., Hechler, R. M., Fussmann, G. F., & Cristescu, M. E. (2022). Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions. Molecular Ecology Resources. doi: 10.1111/1755-0998.13655.
Kirk, K. L. (2012). Biochemistry of the elemental halogens and inorganic halides. Springer Science & Business Media. 1st ed. 1991 edition (March 19, 2012), Pp. 1-312.
Kumari, M., & Gupta, S. K. (2019). Response surface methodological (RSM) approach for optimizing the removal of trihalomethanes (THMs) and its precursor’s by surfactant modified magnetic nanoadsorbents (sMNP)-An endeavor to diminish probable cancer risk. Scientific Reports. 9(1): 1-11.
Lebreton, J. D., Burnham, K. P., Clobert, J., & Anderson, D. R. (1992). Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological Monographs. 62(1): 67-118.
Mona, S., Khalid, M., Jawad, M., Noreen, S., & Rakha, A. (2019). Forensic entomology: a comprehensive review. Advancements in Life Sciences. 6(2): 48-59.
Nayek, U., Unnikrishnan, V. K., Abdul Salam, A. A., Chidangil, S., & Mathur, D. (2020). Thermal energy electrons and OH-radicals induce strand breaks in DNA in an aqueous environment: Some salts offer protection against strand breaks. The Journal of Physical Chemistry A. 124(8): 1508-1514.
Nieves‐Colón, M. A., Ozga, A. T., Pestle, W. J., Cucina, A., Tiesler, V., Stanton, T. W., & Stone, A. C. (2018). Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments. American Journal of Physical Anthropology. 166(4): 824-836.
Shrode, L. D., Tapper, H., & Grinstein, S. (1997). Role of intracellular pH in proliferation, transformation, and apoptosis. Journal of Bioenergetics and Biomembranes. 29(4): 393-399.
Wang, W., Luo, J., Zhong, Y., Lin, X. Z., Shi, H. B., Zhu, J. J., & Zhao, W. S. (2012). Goat liver X receptor α, molecular cloning, functional characterization and regulating fatty acid synthesis in epithelial cells of goat mammary glands. Gene. 505(1): 114-120.
Wu, L., Yick, K. L., Ng, S. P., & Yip, J. (2012). Application of the Box–Behnken design to the optimization of process parameters in foam cup molding. Expert Systems with Applications. 39(9): 8059-8065.
