April 2015

Event Date: 
Wednesday, April 29, 2015 - 18:00 - 18:15
Institution: 
University of New South Wales (UNSW)
Title: 

Bacterial secondary metabolite prodigiosin inhibit biofilm development by cleaving extracellular DNA

Abstract: 

Prodigiosin a bacterial secondary metabolite is a heterocyclic compound belongs to the class of tripyrrole, synthesized by various strains of bacteria includes Serratia species. Research on prodigiosin is under limelight for past 10 years from clinical and pharmacological aspects in relevance to its potential to be drug for cancer therapy by inducing apoptosis in several cancer cell lines. Reports suggest that prodigiosin promotes oxidative damage to DNA in presence of copper ion and consequently lead to inhibition of cell-cycle progression and inducing cell death. However, prodigiosin has not been previously implicated in biofilm inhibition. We performed experiments to reveal any link between prodigiosin and biofilm inhibition through degradation of extracellular DNA which plays a major role in biofilm establishment. Our study showed that prodigiosin (extracted from Serratia culture) has strong DNA cleaving property but does not intercalate with nitrogenous bases of DNA. Using P. aeruginosa PA14 wild-type strain as a model organism we showed that bacterial cells treated with prodigiosin showed significant reduction in its cells surface hydrophobicity and consequently affecting surface energies and physico-chemical property essential for bacterial adhesion and aggregation. We also found that prodigiosin did not influence planktonic growth of P. aeruginosa however, was successful in inhibiting the establishment of biofilms includes decrease in biofilm thickness, adhesion to substratum, decrease in biovolume, microcolony formation and also significantly dispersed pre-established biofilm of P. aeruginosa. This novel function on the biofilm inhibition of prodigiosin could be used to interfere with risks associated with bacterial biofilms. 

Event Date: 
Wednesday, April 29, 2015 - 18:15 - 18:30
Institution: 
University of Southern Maine
Title: 

Developing MicroPIE and a Microbial Ontology

Abstract: 

The study of the evolution of microbial traits requires both phylogenetic as well as phenotypic trait information (also called phenomics). Next generation sequencing has enable high throughput (meta)genomic analyses, but collecting phenotypic information, either de novo or from published taxonomic literature, to create character matrices is still tedious and time-consuming. I am part of a team of researchers developing tools to provide faster collection of microbial phenomic information from published literature. We have created a natural language processing tool, Microbial Phenomics Information Extractor, or MicroPIE, that uses existing parsers, machine-learning tools, and a library of microbial-specific terms derived from ~1000 taxonomic descriptions from the Archaea, Bacteroidetes, Cyanobacteria, and Mollicutes. We have also developed an ontology of terms found in prokaryotic taxonomic descriptions, that is organized using a formal logical framework. This ontology will be used to assist MicroPIE in character identification and extraction, facilitate the identification of trait synonyms used in prokaryotic taxonomic descriptions, and to populate character matrices with higher-level character states. The taxon-character matrices extracted using MicroPIE can be combined with phylogenomic trees and analyzed using the Arbor software package, which is a scalable, web-services based platform for conducting phylogenetic comparative analyses to test evolutionary hypotheses. I’ll show some preliminary results from an analysis of trait evolution in cyanobacteria.

 

Event Date: 
Wednesday, April 29, 2015 - 19:00 - 19:45
Institution: 
University of Southern California
Title: 

Bridging the gap between functional genes and biogeochemistry: a DMSP case study

Abstract: 

A large fraction of the surface ocean food web is active in producing and cycling both dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS).  In addition to the potential climatic significance of DMS production, the role that these compounds play in mediating ecosystem dynamics remains unknown.  An interdisciplinary dataset of biological, chemical and physical measurements was used to test current hypotheses of the role of light and carbon supply in regulating upper-ocean sulfur cycling in oligotrophic regions. Our results suggest that UV-A radiation dose plays an important role in both phytoplankton DMS production and bacterial DMSP degradation. We suggest a modified ‘bacterial switch’ hypothesis where the prevalence of different bacterial DMSP degradation pathways is regulated by a complex set of factors including carbon supply, temperature, and UV-A dose. Finally, numerical models of varying complexity were used to link genetic and enzyme data to biogeochemical rates.