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Teaching: Curriculum Samples Biology 475: Molecular
Biology Lab, offered every other spring (lecture taught by Dr. Turner) Course Evolution Statement Since Fall 2001, this Biology Degree elective/Molecular Biology Degree requirement has only been taught twice. As has been the case since 1997, Dr. Turner taught lecture and I taught lab. Despite dwindling enrollment (7 in 2003, 3 in 2005), I have continued to make many significant lab revisions, most as a result of grant-supported equipment acquisition. These include the addition of DGGE (Denaturing Gradient Gel Electrophoresis) assessment tools, macroarray hybridization materials, and DNA sequencer upgrades (networking capabilities and new software for 4 student lab stations). More information about these methods and their utility/applications are described below. Course Materials Evolution Statement As with my last review, all lab materials represent original curriculum and procedures I have developed based on current Yellowstone-based research in my lab (previous curricula were published in 2002: Boomer, S.M., D. P. Lodge, B.E. Dutton, 2002. Bacterial diversity studies using the 16S rRNA gene provide a powerful research-based curriculum for molecular biology laboratory. Microbiology Education/ASM Press, 3:18-25). In addition to previously reported labs emphasizing DNA isolation, PCR, cloning, sequencing, specific new lab activities in 2003 included a simple non-research plasmid mapping exercise to improve problem-solving/math skills (week 2), and well as sophisticated macroarray-based hybridization and DGGE tools, both allowing more rapid and advanced screening of different DNA-represented populations. In terms of the former, each student vacuum dot-blotted 10 different DNA clones (plus controls) from generated libraries onto 3 filter replicates. They then used three different bacterial group-specific DNA probes to assay for the presence of All Bacteria, Green Phototrophs, and Red Phototrophs. All probes were covalently attached to a unique antigen that, when mixed with commercially-prepared antigen-specific enzyme-linked antibodies and substrate, turned appropriate dot-blot spots purple. Clone library screening methods were also updated in 2005 to include Southern Blotting procedures - in which students separated DNA clones on a gel, blotted the gel onto filter paper, and probed the blotted paper as described above. In contrast with previous slower clone library generation
and analysis (which took 8 weeks of the term for classes run through 2001),
DGGE - a more rapid population genetic assessment method - allowed students
to analyze community diversity and explore alternative gel-based methods over
2 lab sessions. After PCR-amplifying
diagnostic ribosomal gene fragments from To incorporate new labs/methods above, I eliminated a 2-week computational/phylogenetics project - mostly because I had effectively incorporated it first into Computational Biology (Biology 301) and then into General Microbiology (Bi331). Reagent improvements in the field also allowed students to complete plasmid isolation in half a lab (where, before, it had taken 2 sessions). Given new lab computers and digital equipment, I eliminated previous hard-copy research poster assignments, replacing them with on-line individual reports. Despite all the new technology, however, I continue to require rigorous, hand-written individual lab notebook assignments - which include prescriptive pre-lab work and detailed analyses. I also added reading assignments in both 2003 and 2005, requiring students discuss and incorporate relevant research applications from other biological systems using primary publications in their final lab reports. Despite satisfaction bringing new technology and curricula to this course, I have serious concerns about the sustainability and relevance of Molecular Biology as it - or my training - currently exists. First and foremost, providing this much set-up and materials to less than 4 elite students seems a costly and inefficient practice. Second, much as I'd like to tout these methods as cutting edge, the reality is that PCR, cloning/sequencing, and DGGE are old hat to the point that they fundamentally just diagnostic tools which better serve and represent Medical Microbiology and Microbial Ecology (where I will be using them variously in the future). In my opinion, this lab would be better suited for adaptation to a DNA techniques class with fewer pre-requisites, serving both Biology majors as well as well-equipped Chemistry and Forensic Chemistry majors or minors. A "real" Molecular Biology lab course, on the other hand, should be incorporating more genomic level analysis - both of which are beyond my training and equipment repertoire at this time. Consequently, I am pursuing - in earnest and with ongoing support from my NSF/MO mentors/collaborators - a sabbatical during 2008 to develop these skills. Provided Curricula Samples |