Novel Methods for DNA Screening and Analysis using Rapid DNA, Epigenetics, and Digital Polymerase Chain Reaction

Authors

Nicole Fernandez Tejero, Florida International UniversityFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Chemistry

First Advisor's Name

Bruce R. McCord

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

Sara Casado Zapico

Second Advisor's Committee Title

Committee Member

Third Advisor's Name

Anthony P. DeCaprio

Third Advisor's Committee Title

Committee Member

Fourth Advisor's Name

George T. Duncan

Fourth Advisor's Committee Title

Committee Member

Fifth Advisor's Name

Steven B. Lee

Fifth Advisor's Committee Title

Committee Member

Sixth Advisor's Name

Jeffrey D. Wells

Sixth Advisor's Committee Title

Committee Member

Keywords

DNA, Epigenetics, digital PCR, DNA methylation, Microwave extraction, Rapid DNA, High Resolution Melt Analysis, Pyrosequencing

Date of Defense

6-29-2023

Abstract

The main objective of this dissertation project is to develop improved methods for identifying and describing forensic DNA trace levels. The three main goals of the thesis are to improve the ability of rapid DNA analysis for trace samples, develop epigenetic markers for the identification of trace body fluids, and develop a quick and automated method for the detection of incredibly low levels of fecal contamination-related bacteria.

First, prior to a rapid DNA analysis, we developed a quick microwave-based extraction technique that enhances the ability to find low template samples even more. The unique approach generally gives users a technique to enhance the recovery of alleles when low template samples are examined with Rapid DNA equipment.

Additionally, the effect of the sampling location, collection method, and level of methylation on saliva markers of four genes, BCAS4, SLC12A8, SOX2OT, and FAM43A, was investigated. This study highlighted the significance of investigating various body fluid collection/deposition techniques for creating epigenetic markers. For skin/sweat, when using WDR11, PON2, and NHSL1 it showed the potential of high-resolution melt analysis to identify and detect skin/sweat DNA in various bodily fluids.

Finally, singleplex amplifications were created for the investigation of fecal bacterial contamination using nanoplate digital PCR-based technology that could be used to detect fecal contamination in agriculture.

The combination of these approaches will be extremely beneficial to forensic laboratories by increasing the number of sample types that can be evaluated and the amount of information that researchers can gather after an analysis.

Identifier

FIDC011174

ORCID

0000-0001-6908-938X

Previously Published In

Fernandez‐Tejero, N., Gauthier, Q., Cho, S., & McCord, B. R. (2022). High-resolution melt analysis for the detection of skin/sweat via DNA methylation. Electrophoresis.

Recommended Citation

Fernandez Tejero, Nicole, "Novel Methods for DNA Screening and Analysis using Rapid DNA, Epigenetics, and Digital Polymerase Chain Reaction" (2023). FIU Electronic Theses and Dissertations. 5390.
https://digitalcommons.fiu.edu/etd/5390