BACTERIOPHAGE DISCOVERY

Discovering and characterizing novel soil bacteriophages.



Past Projects



Bacteriophage Annotation

Project #1


The discovery and characterization of 10 novel Rhodobacter capsulatus bacteriophages.



Online Bacteriophage Database

Project #2


User-friendly access to store and organize bacteriophage information.


Project #1


Annotation and analysis of potential ATP-dependent DNA helicase gene in bacteriophage "MrWorf"


Undergraduate Research Project Abstract



As more viruses are being discovered, there is a demand to understand the genetic composition of these particles. Prior to this study, none of the genes in bacteriophages that infect Rhodobacter capsulatus have been tested for gene function. Gene 18 of R. capsulatus bacteriophage MrWorf shows potential for encoding an ATP dependent DNA helicase. This is an enzyme which is vital in biological processes such as repairing DNA, replication, and recombination. The gene of interest was amplified via PCR using gene specific primers, cloned into the pET-14b vector, and transformed into competent cells. The cells were induced by IPTG to express the protein product of gene 18 and after purification by HisPur TM Cobalt Spin Column, SDS-PAGE analysis revealed purification to be successful. Further work will need to be conducted to reveal the relationship between gene 18 protein product and ATP-dependent DNA helicase.

ADDITIONAL RESOURCES


Project #2


Development of two user-friendly bacteriophage databases for undergraduate researchers


Undergraduate Software Development Project Overview



With ongoing work through the SEA-PHAGES program (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science), new bacteriophages have been sequenced and need to be annotated. Completion of genome annotation of these newly discovered bacteriophages have led to several new NCBI database entries for bacteriophage discoveries. In addition to annotation of several bacteriophages, there was a need to create a database specific to R. capsulatus bacteriophages that can be easily accessible via the web. While previous work had been done by Dr. Richard Alvey and students at Illinois Wesleyan University to create a database, accessibility to the database had been a challenge. Due to these issues, I created an online database specific to R. capsulatus bacteriophages, making uploads of new bacteriophage annotations easier and more accessible to students. This online database will also prevent repetitive annotation errors and promote more accurate genome annotations for future SEA-PHAGE projects.

Furthermore, the need arose to create a new database using MySQL, the relational database system currently being used by IWU's server. Although I had been using MongoDB, a non-relational database, I modified the preexisting online platform to accomodate the MySQL relational database so that the website could be hosted locally.

ADDITIONAL RESOURCES