Term Project


Description

The term project is due date is April 26th (section 001) or 27th (section 002) at 1:30PM, and is worth 100 points. Students are encouraged to help each other on the project, but must turn in only their own work.

The term project is a molecular phylogenetic analysis of at least one unknown specie isolated in lab. Each student has isolated at least a couple of organisms from their own samples, then attempted to amplify ssu-rDNA from some of these. Any of these that contained an appropriate-sized PCR product (1kbp) were sent to Eton in the RTP (one of the guys there is an ex-NCSU student) for sequencing with 515Fshort, a short version of one of the primers used to obtain the DNA by amplification. These sequences are the starting point for a molecular phylogenetic analysis.


Requirements

The term project you turn in must contain the following items - THIS IS A CHECKLIST! Each of the major headings below are links to detailed directions for that section.

These first items should be bundled together and attached IN ORDER as "Supplemental data". If you analyze more than one organism, include the data (in order) for each organism as separate "packets" - one for each organism.

    • A summary of the microbiological information about your isolate(s).
    • A printout of the raw data from your sequencing reaction(s) (the .pdf file) with the reliable region of this sequence (from the unknown.txt file) highlighted.
    • A printout of the .txt file(s) trimmed from the .seq file, i.e. the file(s) you uploaded to the RDP.
    • A printout of the Sequence Match results.
    • A printout of the sequence(s) most similar to yours identified in this Sequence Match.
    • A printout of the Classifier results.
    • A draft phylogenetic tree containing your sequence(s), its closest relatives, and related species, genera, &c.
    • A final tree containing your sequence(s), the sequences closely related to your sequences, and other representative sequences, with your sequence highlighted and each phylogenetic group indicated.

The last item is the paper itself:

    • Intro
    • Results
    • Discussion
    • Citations

Details about each of these are in the directions pages.