Biology

Event Date: 
Wednesday, July 29, 2015 - 18:15 - 18:30
Institution: 
Australian Institute of Marine Sciences
Title: 

Coral Reefs Go Viral: Unveiling the viruses associated with corals in a changing climate.

Abstract: 

Viruses are the most common biological agents in the global oceans, with numbers typically averaging ten billion per litre. The ability of viruses to infect all organisms indicates they most likely play a central role in marine ecosystems and have important consequences for the entire marine food web. Marine viruses influence many biogeochemical and ecological processes, including energy and nutrient cycling, host distribution and abundance, and horizontal gene transfer events. Research into viruses associated with coral reefs is a newly emerging field. Corals form an obligate symbiotic relationship with the dinoflagellate genus Symbiodinium, upon which the coral relies heavily for nutrition and calcification. Disruption of this symbiosis can lead to loss of the symbiotic algae from their host, resulting in coral bleaching and, if the symbiosis cannot re-establish, death of the coral colony. While a number of factors, including elevated reactive oxygen species production by Symbiodinium have been linked to coral bleaching, viral infection has not been methodically examined as a possible cause. Viruses that potentially target the algal symbiont, Symbiodinium sp., have been reported previously; therefore, we examined whether Symbiodinium in culture is host to a virus that switches to a lytic infection under stress, such as UV exposure or elevated temperature. Analysis of algal cultures, using techniques including flow cytometry and transmission electron microscopy, revealed prevalent viral activity, regardless of experimental conditions. This talk will present recent results and results allow for the development of molecular diagnostic probes for rapid detection of viruses in field samples, and will help monitor and assess the role of viruses in coral bleaching and holobiont functioning.

Event Date: 
Wednesday, July 29, 2015 - 18:00 - 18:15
Institution: 
University of New South Wales
Title: 

Host-virus Interactions in a Frigid, Hypersaline Antarctic Lake Revealed by Metaproteomics

Abstract: 

Deep Lake is a marine derived, hypersaline system in Antarctica that remains perennially ice-free with water temperatures dropping to -20°C. These harsh environmental conditions have led to a low complexity microbial community, completely dominated by members of the haloarchaea, including four isolated species (tADL, DL31, Hrr. lacusprofundi and DL1) that account for ~72% of the lakes cellular population. Genomic sequencing and analysis of the four isolated species combined with metagenomics have revealed an unprecedented level of inter-genera exchange of long (up to 35 kb) stretches of identical DNA. However, despite the rampant, promiscuous exchange of DNA, distinct haloarchaeal lineages appear to prevail in the lake by virtue of their unique capacities for niche adaptation (1, 2). With no apparent metazoan grazers present in the lake, viruses are hypothesised to play a dominant role in shaping the microbial community of Deep Lake. In this present study we applied metaproteomics for the first time on a hypersaline environment and combined it with in-depth genomic and metagenomic analysis of Deep Lake CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) and BREX (Bacteriophage Exclusion) (3) systems to elucidate host-virus interactions.
Shotgun metaproteomics was performed on Deep Lake biomass from 5 distinct depths, captured by sequential filtration through 3 µm, 0.8 µm and 0.1 µm filters during the Antarctic summer of 2008/2009. All identified proteins were manually annotated and grouped into taxonomic and functional categories. We characterized CRISPR systems of the four genomes and the Deep Lake metagenome and used CRISPR spacer and repeat sequences to identify sources of invading DNA.
The Deep Lake metaproteome comprised around 1100 detected proteins. A striking feature was the identification of multiple, highly abundant cell surface proteins with a high degree of sequence variation compared to the genomes of the isolate species (“variants”). E.g. we identified 6 distinct proteins all matching the main S-layer component of tADL. Furthermore we detected variants for archaella (archaeal flagella), pili and other cell surface proteins. Multiple viral proteins were detected with sequence similarity to other, mainly haloarchaeal viruses. Functional CRISPR loci could be identified in the genomes of all four isolated species and CRISPR-associated (Cas) proteins were detected for two of them. CRISPR spacers could be linked to different sources of invading DNA, with most, but not all spacers targeting viruses. We detected one BREX protein (PglX) for Hrr. lacusprofundi. Some detected proteins, including cell surface proteins, were encoded on metagenome contigs together with putative viral genes.
The detection of multiple protein variants for cell surface structures like S-layer and archaella is indicative of phylotypes that are present in the lake. Introducing variation in cell surface structures likely provides the haloarchaeal populations with a way of evading viral infection. Consistent with this is the presence of a diverse viral population in Deep Lake. We detected proteins from at least eight distinct haloarchaeal viruses (eight major capsid proteins), with some proteins confirming active viral life cycles (e.g. prohead protease). Furthermore, the CRISPR spacer analysis revealed that some viruses infect multiple species (broad host range). In addition to the acquired cell surface variation, haloarchaeal host cells have employed active CRISPR and BREX systems as defense against viral infection.                             The presence of cell surface genes on metagenomic contigs together with putative viral genes, and the high degree of sequence variation observed in many cell surface proteins, suggests that viruses are involved in the acquisition, mutation and distribution of cell surface variants within the haloarchaeal populations. Overall, we were able to identify and describe a complex network of virus-host interactions, revealing a pivotal role of viruses in shaping the microbial community in Deep Lake (4). 
 

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. 

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 - 18:00 - 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, 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 - 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, March 25, 2015 - 19:00 - 19:45
Institution: 
University of Sydney
Title: 

Poxviruses: Man’s Best Friend. (Or How I Learned to Stop Worrying and Love the Virus)

Abstract: 

 

Poxviruses and humans have had a chequered past. Once the scourge known as smallpox routinely devastated human populations, some estimates are as high as 200 million mortalities last century. However the discovery of a tame version of the virus led to Edward Jenner to demonstrate the practise we now know as vaccination, which has gone some way to repairing the reputation of this virus. My research is built on the premise the these viruses still have much to teach us about many aspects of virology and host cell biology. And one of the most novel and exciting applications may be just around the corner.

 

Syndicate content