Webb, Bruce A

The Webb Laboratory focuses on Lepidopteran viruses - specifically Nudiviruses which are DNA viruses that are sexually transmitted.  This project entails screening sequenced lepidopteran genomes for evidence of nudiviruses so that new pest control strategies can be developed based on sterilizing pathology of these sexually-transmitted viruses.

Students:

Emrah Ozel, PhD Student, will work on the cluster to detect and identify Nudivirus-like genomic fragments in Lepidopteran samples that are uploaded to public databases such as NCBI SRA database.

Computational methods:

Our computational method relies on downloading data from the database using fasterq-dump package and assembling short reads using various software freely available at UK such as HiSAT and Bowtie.

Software:

Emrah Ozel: Fasterq-dump, HiSAT, Bowtie, Tophat, SRAToolkit, Trim Galore, and SAMTools.

UK and non-UK collaborators:

HzNV Screening Using Bioinformatic Tools

Recently, we analyzed more than 650 separate SRA experiments to search for traces of possible HzNV infection in NGS datasets of three species (H. zea, H. armigera, H. virescens) uploaded to public databases. This computationally intense analyses were performed on UK’s Lipscomb Cluster Computer and yielded more than 3000 individual short-reads that maps on HzNV genome without any mismatches. This method will be extended to cover other major Heliothine pest species.

Using Advanced Tools to Discover Novel Heliothine Viruses

In this section, I will run a de novo assembly pipeline to generate contigs that are exogenous to host genome and utilize annotation tools to identify origin of these contigs. These pipelines and programs can help us to identify novel viruses and/or elements of host microbial fauna.

Assessing Gene Expression Differences in Public SRA Databases 

Lastly, based on the evidence we have collected from publicly available datasets, we think it is possible to study gene expression differences between infected and uninfected Heliothine insects using these public datasets. Considering the sheer size of transcriptomic SRA data (H. armigera) uploaded to NCBI database and  the bioinformatic tools that allow us to distinguish infected and uninfected samples, a very basic differential gene expression analysis can be performed with these datasets.

Grants:

Webb, Bruce NIH 092013 SBIR: Biological methods for enhancing wound healing properties. $52,239 ParaTechs Corp 9/30/2013 9/19/2014

Publications:

Patents: