Browsing by Subject "automation"
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Item Genetic profiling of skin microbiomes for forensic human identification(2017-12-01) Schmedes, Sarah E.; Budowle, Bruce; Ge, Jianye; He, Johnny J.The field of microbial forensics has expanded from a focus in biodefense and biocrime attribution to include various metagenomics and microbiome applications made possible by advancements in sequencing and bioinformatics technologies. Recent developments in metagenomics and microbiome research with application to the forensic sciences, include post-mortem interval, body fluid identification, recent geolocation, and human identification. The primary goal of the dissertation described herein was to assess the feasibility of human identification from skin microbiomes using both shotgun metagenomic sequencing and targeted enrichment strategies. The main studies of this dissertation were conducted under the hypothesis that genes from stable, universal microbial species from the core skin microbiome can differentiate skin microbiomes of individuals and be applied towards forensic human identification purposes. The initial study presented describes the development of a tool, AutoCurE, used to identify errors in bacterial genome metadata from public databases and curate the data for subsequent use in comparative genomic studies. This study highlights the types of inconsistencies and errors which may be present in public genome databases and describes the development of a curated local bacterial database for use in subsequent studies. This doctoral research herein presents the development of a novel approach for human identification using stable, universal clade-specific markers from skin microbiomes. Initially, publically available shotgun metagenomic datasets generated from skin microbiome samples collected from 17 body sites from 12 individuals, sampled over three time points over the course of ~3-year period, were mined to identify stable, universal microbial markers. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification, were performed using the nucleotide diversities of clade-specific markers to predict the correct classification of skin microbiomes to their respective host individuals. Reduced subsets of markers were developed into a novel targeted metagenomics sequencing panel, the hidSkinPlex, to generate individual-specific skin microbiome profiles to use for human identification. Finally, the hidSkinPlex was evaluated on skin microbiome samples collected from eight individuals and three body sites, in triplicate, to demonstrate a proof-of-concept to differentiate individuals with high accuracy. The hidSkinPlex, comprised of 282 bacterial and 4 phage markers from 22 family-, genus-, species-, and subspecies-level clades, was used to correctly identify skin microbiomes from their respective donors with up to 92%, 96%, and 100% accuracy using samples from the foot, manubrium, and hand, respectively. Additionally, skin microbiomes were classified with up to 97% accuracy when the body site was unknown, and body site origin could be predicted with up to 86% accuracy. The hidSkinPlex is the first targeted metagenomics sequencing panel and method designed specifically for skin microbiomes with the intent of forensic human identification applicationsItem Optimization of Spermatozoa Capture During the Differential Extraction Process for STR Typing with the Potential for Automation(2002-05-01) Marshall, Pamela L.; Eisenberg, Arthur; Martin, Michael W.; Wordinger, Robert J.Marshall, Pamela. Optimization of Spermatozoa Capture During the Differential Extraction Process for STR Typing With the Potential for Automation. Master of Science (Forensic Genetics). May, 2002. In 1998, within the United States, it is estimated that a rape occurred every 2.3 minutes. In 1995, according to the Bureau of Justice Statistics, an estimated 350,000 rapes or sexual assaults (R/SA0 were experienced by persons age 12 or older. Of the estimated 100,000 R/SA reported, there were only approximately, 25,000 cases analyzed by crime labs nationwide. The majority of crime laboratories throughout the U.S., especially those in major metropolitan cities, have a significant backlog of unresolved R/SA cases. With the implementation of the Convicted Offender Database (CODIS), it is essential that all R/SA cases by analyzed, especially those lacking a known suspect. The comparison of the short tandem repeat (STR) profiles derived from sperm DNA recovered from evidentiary material with CODIS samples would provide the police with critical investigative leads resulting in the identification of the assailant. The goal of this research is to develop a cellular sorting method for the isolation of sperm cells from sexual assault samples which will: 1) take advantage of differentiating features (extracellular antigenic sites) for complete separation of cell types, 2) provide a more efficient means of sperm recovery, increasing DNA yield from the male fraction, and 3) ensure the DNA isolation process is compatible with the amplification of the CODIS core STR loci. Overall, the proposed technique will increase the probability of success in the analysis of sexual assault case samples. (NIJGrant #: 2000-IJ-CX-K009).