Bing He and Joshua Fletcher will present their research on March 15th, 2012
Background for Bing He’s talk :
Identify enhancer-promoter associations in Drosophila
Transcriptional enhancers play an essential role in establishing cell type and developmental stage specific gene expression patterns in metazoans. They typically comprise multiple transcription factor (TF) binding sites (TFBS) located in DNA regions of a few hundred base pairs. To date, mechanisms of enhancer action are still poorly understood and a key gap in our knowledge is how enhancers select specific promoters for activation. To fill this gap we aim to develop an integrative approach to computationally predict enhancer-promoter associations followed by experimental validation in Drosophila melanogaster. Our preliminary results based on a set of experimentally verified enhancer-promoter pairs show that several features can be extracted from ENCODE data and are effective in discriminating between real and random enhancer-promoter associations. These features include activity profile correlation, TF-target expression correlation and distance constraint between enhancers and target promoters. They can be integrated to construct a statistical predictor for enhancer and promoter association. The proposed work will have significant impact on multiple aspects of enhancer research such as the basic mode of action of enhancers and their involvement in disease etiology.
Background for Joshua Fletcher’s talk :
Identification of novel virulence factors of Francisella tularensis
Francisella tularensis is a Gram negative intracellular pathogen with diverse eukaryotic hosts. Its low infectious dose, high mortality rate, and weaponization by the USA, Japan, and the former Soviet Union during World War II and the Cold War have led to its classification as a Class A Select Agent by the CDC. The extreme virulence of F. tularensis is due, in part, to its capsule and atypical lipopolysaccharide as well as its ability to subvert the immune response to avoid killing. Francisella has a ~30 kb locus termed the Francisella Pathogenicity Island (FPI) that encodes genes important for phagosome escape, although the mechanisms underlying this process are unclear. Several immune system subversion mechanisms of bacterial pathogens are mediated by effector proteins that are delivered through sophisticated secretion systems. Unlike other intracellular pathogens such as Legionella and Salmonella, the Francisella genome does not appear to encode common secretion systems (Type III, Type IV, etc.) or their associated effectors, although some evidence exists for a putative Type VI apparatus encoded in the FPI. The subversion of the host response (inhibition of oxidative burst, degradation of the phagosome, etc.) is an active process requiring live bacteria, indicating that while LPS and capsule contribute to immune evasion, other Francisella factors that are still undiscovered, play important roles in virulence. To identify these factors a combined bioinformatics and transposon mutagenesis approach was used to generate a list of 24 candidate effectors. One such candidate was ORF FTT0613c, which has significant similarity to virK, a secreted effector found primarily in plant pathogens and symbionts and thought to interact with host proteins. A virK mutant in the Live Vaccine Strain (LVS) of F. tularensis subsp. holartica has significantly decreased uptake in the murine macrophage-like J774 cell line. Future work on this gene will include characterization of the mutant in the highly virulent Schu S4 strain, development of assays for detection of secretion, and identification of protein-protein interactions both in Francisella, and in the host. In parallel, an effort to mutagenize and characterize the other candidate effectors is underway.