AUG 22, 2019 10:30 AM PDT

Generating Authentic Research Experiences of Forensic-Based Projects in an Undergraduate Classroom Laboratory

C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Professor of Biology, Eastern Michigan University
    Biography
      David Kass received his PhD in Biological Sciences from the University of South Carolina combining his interests in molecular genetics and evolution, finding a relationship between concerted evolution of interspersed repetitive elements and speciation of Peromyscus. These elements were eventually determined to be part of the L1 LINE retrotransposon with the concerted evolution primarily resulting from retrotransposition of new copies from a few source genes. As a Postdoctoral Fellow, Dr. Kass worked on rodent and primate SINEs to gain insights into their genetic and evolutionary impacts and to date has continued SINE and LINE investigations. His research has led to discovering the first clear-cut example of an Alu gene conversion event; identified recent integrations of SINEs in rodents and humans; incorporated SINEs into human population studies; identified new mammalian SINE and LINE families with incorporation into evolutionary studies; and developed Alu-based PCR tetraplexes as a simple tool for generating complex DNA profiles. We now know, from the Human Genome Project that nearly half the human genome consists of transposable element sequences (mostly retrotransposons) and remain active, thereby continuing a role in the dynamics of the genome plus contributing to medical disorders. Therefore Dr. Kass was working with "junk DNA" before it was cool to. As a faculty member at a predominantly undergraduate institute (PUI), a primary focus has been the development of a Genome Analysis laboratory course incorporating his work into authentic research experiences for increasing the number of students experiencing actual scientific investigations.

    Abstract

    DNA profiling tools to teach undergraduate students about forensics generally utilize the PV92 Alu and D1S80 VNTR markers, but are both limited in scope. In contrast, advanced profiling systems are costly and not practical for undergraduate laboratory courses. Therefore, I have designed a DNA profiling system for use in mid- to upper-level UG laboratory courses. Three dimorphic Alu-based PCR tetraplexes were developed that are simple to use, yet yield complex DNA profiles with 531,441 possible outcomes. This profiling system allows students to study forensics, paternity, human populations, and may have potential use in determining ancestry. A corresponding web site was developed to incorporate and analyze the generated data. In addition, I have designed a second project based on the concerted evolution of mammalian L1 elements yielding forensic and evolutionary data. This project involves student generated intra-L1 PCR DNA libraries, which are biased for “younger” elements, and utilizes a toolbox of standard molecular genetic techniques and bioinformatic tools. Students query sequences from individual clones via GenBank to identify the organism (or related organism) of the DNA source. Students can also generate a molecular phylogeny of sequences to contrast to known phylogenetic relationships of mammals, and will be the basis of a long-term project to produce a mammalian tree-of-life. These projects, suitable for genetics, molecular genetics, or genomics laboratories represent the initial phase for developing large-scale consortium-based projects.

    Learning Objectives: 

    1. Defining retrotransposons and their contributions to the dynamics of mammalian genomes
    2. The use of retrotransposons as tools in analyses of forensics, ancestry, population genetics, and evolution


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