Microbial Genomics: Wet Lab Experiments to Validate Gene Calls in Kytococcus Gene Annotation

gene sequence.

This project will take hypotheses developed by bioinformatics-based investigations to wet lab validation.

Project description

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.

Project outcome

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.

Project details

Timing, eligibility and other details
Length of commitment About a semester (3-5 months)
Start time Anytime
Level of collaboration  Small group project (2-3 students)
Benefits Academic Credit
Who is eligible All undergraduate students; completion of an undergraduate biochemistry course desired, but not required
Goldwater and the National Science Foundation

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.

Project mentor

Stephen Koury

Associate Professor

Biotechnical and Clinical Laboratory Sciences

312 Farber Hall, South Campus

Phone: (716) 829-5188

Email: stvkoury@buffalo.edu

gene description on a computer .

This figure illustrated the results of the two top BLAST search results when the Ksed_02850 amino acid sequence (Query) was used to search the nr BLAST database.

another image of gene sequencing.

This image is what was seen when blasting the amino acid sequence beginning at the first potential upstream alternate start codon.

Start the project

  1. Email the project mentor using the contact information above to express your interest and get approval to work on the project. (Here are helpful tips on how to contact a project mentor.)
  2. After you receive approval from the mentor to start this project, click the button to start the digital badge. (Learn more about ELN's digital badge options.) 

Preparation activities

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. 

  • Read the paper describing the sequencing and computer pipeline annotation of the Kytococcus sedentarius genome. This is available as a free full text download from PubMed at the following link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035214/
  • Additional preparation will take place in consultation with Dr. Koury prior to starting research in the lab that will involve materials specific to the gene under investigation as well as lab safety and general laboratory techniques required for successful completing of the project.