May 2015

Event Date: 
Wednesday, May 27, 2015 - 18:00 - 18:15
Institution: 
Macquarie University
Title: 

Whole Genome Engineering in Saccharomyces cerevisiae –An introduction to synthetic biology and the Yeast 2.0 project

Abstract: 

The prevailing ethos in the emerging field of synthetic biology is to understand biology through engineering and re-design. This approach has been directed towards the construction of novel genetic regulatory circuits, altered metabolic pathways, and even whole genomes. The ‘Yeast 2.0’ project is an international synthetic biology collaboration aimed at building a fully synthetic Saccharomyces cerevisiae genome by 2017. Although only modest changes are being made to the natural genome sequence, an inducible evolution system in being incorporated into the synthetic genome that can result in large-scale genomic rearrangements. This ‘Synthetic Chromosome recombination and Modification by LoxP Mediated Evolution’ (SCRaMbLE) system will be used to generate millions of unique genomes with varied architecture and gene content. By placing appropriate selection pressure on SCRaMbLEd populations, cells with minimal genomes or superior industrial properties can be recovered. Sequencing the genomes of these isolates will then be carried out with the goal of revealing novel ‘design principles’ for rational engineering, fulfilling the synthetic biology mandate to learn by building.

Event Date: 
Wednesday, May 27, 2015 - 19:00 - 19:45
Institution: 
University of New South Wales
Title: 

Understanding the roles of non-coding RNAs in Enterohaemorhaggic E. coli pathogenesis

Abstract: 

Expression of virulence genes in pathogenic bacteria is tightly regulated in response to environmental cues at both the transcriptional and post-transcriptional level. RNAs that do not encode proteins (non-coding RNAs) are now appreciated to play important roles in post-transcriptional gene regulation by interacting with mRNAs and modulating translation and stability. High throughput sequencing studies are now uncovering hundreds of non-coding RNAs in pathogenic bacteria and the challenge now is to understand the function of these RNA species.
A major subclass of bacterial non-coding RNA, termed small RNAs (sRNAs), requires the RNA chaperone Hfq to anneal to mRNA targets and effect regulation.  Using UV-crosslinking and NextGen sequencing techniques (CRAC or CLIP-Seq) we have generated high resolution maps of Hfq-RNA interactions in the human pathogen Enterohaemorhaggic E. coli (EHEC). Within this dataset of Hfq binding sites we have identified 55 new sRNAs (Tree et al Molecular Cell) and we are now looking to identify the mRNA targets of these sRNAs and understand their role in pathogenesis.
Recently it has been demonstrated that RNA-RNA interactions can be extracted from CLIP-Seq data allowing ncRNAs to be sequencing in complex with their mRNA targets (a technique termed CLASH). This analysis gives insights into the function of ncRNAs in vivo. Small RNAs have been shown to recruit the RNA endonuclease, RNase E, when duplexed with an mRNA target and we have recently demonstrated that sRNA-mRNA interactions can be sequenced from RNaseE CLIP-Seq data. We have confirmed a subset of these interactions using translational GFP fusions. Using this dataset we have identified mRNA targets for our newly identified EHEC sRNAs and have begun assigning functions to some of these novel RNA species. We have found that the EHEC specific sRNA, Esr41, represses translation of select iron uptake receptors indicating a role in modulating iron availability.

Event Date: 
Wednesday, May 27, 2015 - 18:15 - 18:30
Institution: 
University of Western Sydney & Macquarie University
Title: 

Structure, diel functional cycling and viral ecological filtering in the microbiome of a pristine coral atoll in the Indian Ocean

Abstract: 

Given the role of microbes as both indicators and drivers of ecosystem health, establishing baselines in pristine environments is crucial to predicting the response of marine habitats to environmental change.  Here we describe a survey of microbial community composition and metatranscriptomic gene expression across the Indian Ocean, encompassing the first samples from the pristine Salomon Atoll in the Chagos Archipeligo.  We observed strong patterns in beta-diversty  which reflected  Longhurst biogeographical  provinces established  using primary productivity and thermohaline properties of ocean currents.  Samples from within Salomon Atoll showed a highly unique community which was remarkably different even from adjacent samples despite constant water exchange.  This pattern was driven by the dominance of the photosynthetic cyanobacterium Synechococcus within the lagoon, the diel activity of which was responsible for driving shifts in the transcriptional profile of samples.  Inside the lagoon, increases in the expression of genes related to photosynthesis and nutrient cycling associated with the bottom-up control of bacterial populations, however the expression of viral proteins increased five-fold within the lagoon during the day, indicating a concomitant top-down control of bacterial dynamics byphage.  Indeed, genome recruitment against Synechococcus reference genomes suggested  viruses  provide  an  ecological filter for determining the diversity patterns in this system. This study also represented a proof of concept for  using a ‘citizen oceanography’ approach utilzing tools that may easily be adapted to deployment on any ocean going yacht, greatly expanding the scale and outreach of marine microbiology studies. 
 

Event Date: 
Wednesday, June 24, 2015 - 18:00 - 18:45
Institution: 
University of Western Australia
Title: 

Microbial life in Movile Cave – an unusual cave ecosystem

Abstract: 

Movile Cave (Mangalia, Romania) is a unique cave ecosystem sustained by in situ chemoautotrophic primary production, analogous to deep-sea hydrothermal vents. The cave has been cut-off from the surface for the past 5.5 million years with the primary energy source coming mainly from hydrogen sulfide and methane released from the thermal fluids. Invertebrates, many of which are endemic to Movile Cave, are isotopically lighter in both carbon and nitrogen than surface organisms, indicating that chemoautotrophic primary production, primarily driven by methane and sulfur oxidizing microorganisms, occurs in the cave. In this talk, I will present our recent work on the microbiology of the Movile Cave ecosystem, with particular emphasis on functional diversity of Bacteria involved in aerobic one-carbon (methane and methylated amine) metabolism. Insights from metagenomic and genomic sequence analyses of the microbial community and isolates, respectively, will be discussed in detail.

Event Date: 
Wednesday, June 24, 2015 - 19:15 - 20:00
Institution: 
University of New South Wales
Title: 

The role of quorum sensing in chitin biodegradation

Abstract: 

The 1011 ton global annual turnover of chitin has generated extensive interest in the regulation of chitin processing enzyme production in bacteria. Some bacteria regulate chitinase production by N-Acyl-L-homoserine lactone (AHL) mediated quorum sensing. In this study, a description of bacterial community succession during chitin particle colonisation and depolymerisation in activated sludge is presented. It was discovered that Betaproteobacteria and Bacteroidetes lineages dominate chitin colonisation in sludge and that AHLs bind to chitin at concentrations that upregulate AHL dependent transcription in bacterial cells associated with the chitin surface. There was no requirement for high cell density (a quorum) at the chitin surface. Further, N-Acetyl glucosamine (GlcNAc), the monomer of the chitin polymer, is shown to inhibit AHL dependent gene transcription representing a previously unrecognised mechanism by which the chitinase reaction product negatively regulates chitinase production. Evidence is presented supporting a role for both competitive inhibition at the AHL binding site of LuxR type transcriptional regulators and catabolite repression. The quorum sensing inhibitor activity of GlcNAc adds to its list of possible therapeutic benefits.