This project will take hypotheses developed by bioinformatics-based investigations to wet lab validation.
When microbial genomes are sequenced, computer pipeline annotation of the finished genome takes place to 1) predict where genes are located in the genome and 2) to assign function to genes if possible after they have been called. The genome of the Gram + bacterium Kytococcus sedentarius is being manually re-annotated as part of the course MT447/547, Introduction to Microbial Genome Annotation. A number of potential errors in the pipeline annotation have been hypothesized by bioinformatics-based research performed by undergraduate and graduate students in the course. These findings need to be validated by performing "wet lab" experiments. Activities in the project will involve culture of Kytococcus sedentarius, isolation and analysis of RNA and genomic DNA, PCR, reverse transcriptase PCR, quantitative real-time PCR and some experimental design/interpretation.
Students will be expected to keep a detailed digital laboratory notebook on Dr. Koury's UB Box drive and present their results at regular lab meetings held with core partners. Student wet lab research results will, in addition, be uploaded to gene information pages on the site geni-act.org, for access by other microbial genomics researchers. Data generated of sufficient quality will also be included in manuscripts/presentations at meetings with co-authorship for the student researchers.
|Length of commitment||About a semester (3-5 months)|
|Level of collaboration||Small group project (2-3 students)|
|Who is eligible||All undergraduate students; completion of an undergraduate biochemistry course desired, but not required|
Students participating in this project might be interested in and eligible for the Goldwater Scholarship and the National Science Foundation Graduate Research Fellowship. Connect with the Office of Fellowships and Scholarships to learn more.
If you are planning to use this project to satisfy program requirements for your academic major or minor, it is your responsibility to obtain approval from your academic department prior to beginning the project.
Once you begin the digital badge series, you will have access to all the necessary activities and instructions. Your mentor has indicated they would like you to also complete the specific preparation activities below. Please reference this when you get to Step 2 of the Preparation Phase.