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Research for Non-Researchers: Three Research Projects with (Possible) Clinical Applications

Research for Non-Researchers: Three Research Projects with (Possible) Clinical Applications. Chris Einspahr 2012 ASM/JGI Bioinformatics Institute. The Background. Non-traditional, degree-granting program UTMDACC School of Health Professions Clinical Laboratory Science program

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Research for Non-Researchers: Three Research Projects with (Possible) Clinical Applications

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  1. Research for Non-Researchers:Three Research Projects with (Possible) Clinical Applications Chris Einspahr 2012 ASM/JGI Bioinformatics Institute

  2. The Background • Non-traditional, degree-granting program • UTMDACC School of Health Professions • Clinical Laboratory Science program • Students enter school as college juniors (transfers) • Junior year curriculum • Aggregated class consisting of students from CLS, MGT, HT, CT, CGT programs • General, healthcare-related, upper-level classes

  3. The Background • Senior year curriculum (CLS program) • Didactic and laboratory-based instruction in four main areas of study • Hematology/Hemostasis, Clinical Chemistry, Immunohematology, Diagnostic Medical Microbiology • Skills and knowledge directly applicable to work in clinical laboratories • Preparatory for board certification exams

  4. The Background • Research Projects • In their senior year, students are assigned research projects related to their studies and the clinical lab • Some good, some not so good…

  5. The Challenge • Introduce microbiology-based (perhaps other disciplines?) bioinformatics research projects • Needs to satisfy research project requirements • Poster would be good… • Publication would be great! • Needs to be related (however tangentially) to the focus of our program (CLS) • Needs to begin in the junior year and finish (ideally) before 2nd semester of senior year

  6. The Strategy • Start small, start basic… • Two proposed projects • Metagenomic analysis of oral specimens from cancer patients • Identification of missing or non-functioning genes in M. leprae as compared to other mycobacterial species • Other possible projects • Genetic characterization of bacterial antimicrobial resistance mechanisms • Identification of missing or non-functioning genes in P. jirovecii

  7. The Initial Projects • Metagenomic analysis of oral specimens from cancer patients • Assess the normal oral flora of (oral?) cancer patients and compare to that of “normal” subjects • Compare a sampling of subjects to the data collected by the Human Microbiome Project • Statistical comparison of bacterial populations? • Further studies – sentinel site? • Does a change (if one exists) in bacterial flora constitute an “early warning system?”

  8. The Initial Projects • Identification of missing or non-functioning genes in M. leprae as compared to other mycobacterial species • Mycobacterium species are notoriously slow-growers, but… • Historically, M. leprae has been considered “unculturable” in the clinical setting • Functioning genes in other species but missing in M. leprae may be a key • May be able to take advantage of alternative pathways • Modifications to current media may generate growth

  9. Other Projects • Genetic characterization of bacterial antimicrobial resistance mechanisms • Well studied already, just not by my students • A possible “get to know you” project with students and NCBI

  10. Other Projects • Identification of missing or non-functioning genes in P. jirovecii • Basically the same project as with M. leprae, except the genome has not been fully elucidated • As with M. leprae, developing a culture methodology would be the end goal (another clinically unculturable pathogen)

  11. Questions? Comments? Suggestions? That’s all for now…

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