The primary goal of my research is to generate insight into important questions in biology using bioinformatics and computational biology methods. I am also interested in developing bioinformatics and computational tools for use by the biological community. In addition, I am always ready to assist my colleagues with analysis of large biological data sets as the need arises. I am committed to undergraduate research, and all of my publications as an assistant professor at UNLV include undergraduate students as authors. Outlined below are some of the research projects currently pursued in my lab.
Genomics and lytic mechanisms of Paenibacillus larvae bacteriophages
Paenibacillus larvae is a Gram-positive, spore-forming bacterium that is the causative agent of American Foulbrood Disease (AFB), one of the leading causes of the global population decline of the honeybee (Apis mellifera). P. larvae spores are extremely durable, lasting several decades, and are largely antibiotic resistant, making treatment of P. larvae outbreaks difficult. Currently the only method for eliminating P. larvae outbreaks is the wholesale incineration of infected hives. As bees lack an adaptive immune system, one potential antibiotic-free AFB treatment is the use of bacteriophages that target P. larvae. Phages have several attractive features as a treatment strategy, such as not contaminating honey, being harmless to humans and to important symbiotic bacteria in the larval gut, and co-evolving with their host. In the last year alone five studies were published on treating AFB with P. larvae phages or P. larvae phage endolysins, with promising, if not conclusive, results.
Beginning in 2013, an ever-increasing number of novel P. larvae phage genomes is being sequenced and published. The Tsourkas lab is one of the leaders in P. larvae phage genomics, having published the largest number of P. larvae phages to date and currently collaborating with researchers from Brigham Young University to publish an even larger group of P. larvae phage genomes. This will help us characterize the genomic landscape and understand the evolutionary history of these important phages. The process of phage genome annotation is ideally suited to undergraduate research and we are currently recruiting talented undergraduate students to annotate P. larvae phage genomes for publication.
Tailed bacteriophages typically lyse their host by means of a hydrophobic holin protein that punctures the host plasma membrane and an endolysin that cleaves the host peptidoglycan cell wall. All sequenced P. larvae phages code for a conserved N-acetylmuramoyl-L-alanine amidase, yet a holin has not yet been identified, likely due to the fact that holins are poorly conserved and difficult to identify bioinformatically. As part of our work on P. larvae phage genomes, we have identified several candidate genes that potentially code for proteins with holin function. We plan to test the function of these candidate holins as well as several other interesting genes by creating edited P. larvae phage genomes where genes of interest have been knocked out using CRISPR-Cas. Subsequent experiments will help indicate the role of these genes in host lysis, if any, and eventually identify the lytic mechanisms of P. larvae phages.
A meta-tool for bacteriophage gene prediction and genome annotation
Bacteriophages are the most numerous and diverse entities on Earth, with an estimated 10 31 particles in the biosphere. The rapid decrease in cost of sequencing technology has resulted in an explosion in the number of published phage genomes. Consequently, accurate gene prediction and start codon calling (in cases where a gene has more than one possible start codon) for newly assembled phage genomes is of great importance. There are currently several gene calling programs (Glimmer, GeneMark, GeneMark.hmm) that are widely used to annotate new phage genomes in an automated manner. While producing rapid results, such programs occasionally produce false positives and missed calls (false negatives.) Furthermore, these programs may not necessarily be in agreement in many cases, complicating the process of gene and start codon calling. Accurate genome annotation thus requires manual curation, using additional information such as expert knowledge, BLAST results, gene length, and overlap with other genes (since bacteriophage genes seldom overlap with each other). However, when the number of sequenced phages is large, manual curation becomes prohibitively time-consuming. To this end we are working towards developing a genome annotation meta-tool for bacteriophages that integrates all readily available information to call genes and start codons, thereby combining as many of the advantages of manual curation as possible, while retaining the speed of automation.
SEA-PHAGES at UNLV
We are delighted to announce that UNLV has been selected to be part of HHMI’s SEA-PHAGES program beginning Fall 2017. SEA-PHAGES is an HHMI-funded course based research experience for undergraduates to study, discover, and publish bacteriophage genome sequences. The SEA-PHAGES course consists of two semesters, the first semester being a wet-lab course, and the second a bioinformatics course. In the first semester, students isolate phages from environmental samples, characterize them using electron microscopy, extract and amplify phage DNA and send it for sequencing. In the second semester, students assemble, annotate and publish the phage genome in a peer-reviewed journal. Two students from the course are then selected to present at the annual SEA-PHAGES symposium at HHMI headquarters. The first semester will be co-taught by Dr. Kurt Regner and Dr. Christy Strong. The second semester will be taught by Dr. Philippos Tsourkas, who will also serve as course coordinator and point of contact.
SEA-PHAGES has been highly successful and is currently in its 10th year, with over 100 colleges and universities from across the United States participating. Students that have completed SEA-PHAGES frequently go on to pursue a career in research and schools participating in the SEA-PHAGES course have higher rates of recruitment and retention in undergraduate participation in research in the life sciences. The UNLV SEA-PHAGES team is very excited about bringing SEA-PHAGES to UNLV and looks forward to implementing it.
Bioinformatics, Mathematical Modeling
Ph.D. University of California, Berkeley