Genetics

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, January 28, 2015 - 19:00 - 19:45
Institution: 
University of Sydney
Title: 

The use of genomics in diagnostic and public health microbiology

Abstract: 

Since 2004 technological advances have enabled us to sequence more nucleic acid and generate more data in a shorter amount of time. Decreases in cost per nucleotide sequenced, the initial price of sequencing machines and the complexity of library construction means that whole genome sequencing (WGS) is available in many research labs and an increasing number of public health microbiology labs. I will examine the use of WGS in public health microbiology, particularly the possibility of investigating organisms without culture, the interrogation of genomes where PCR may be unavailable, outbreak investigation, tracking resistance mutations and novel pathogen discovery.

Event Date: 
Monday, February 24, 2014 - 09:30 - Tuesday, February 25, 2014 - 17:00

 

Registration Closed

24-25 February 2014
The Australian Museum

Microbiology is undergoing a revolution bought about by advances in next-generation DNA sequencing technology.  Researchers are now required to understand an array of bioinformatics principles and tools to interpret the vast amounts of data being generated. Presented by leading Australian researchers, TOAST is a 2-day event aimed at postgraduate students and early career postdocs providing in-depth tutorials encompassing concepts and software available to molecular microbiologists and microbial ecologists including:

Event Date: 
Wednesday, July 31, 2013 - 19:00 - 19:45
Institution: 
Australian National University
Title: 

Understanding Secondary Metabolite Biosynthesis as the Key to Unlock New Chemical Diversity in Fungi – from Viridicatumtoxin to the Immunosuppressive Neosartoricin

Abstract: 

The advancement of DNA sequencing technology has unlocked an unprecedented amount of microbial genomic information. These genome sequences also revealed a large number of secondary metabolite (SM) genes in both bacteria and fungi. For filamentous fungi in particular, the number of SM gene clusters encoded in the genome are often beyond the number of compounds that are reported for individual species. This is likely attributed to the tight regulation of the SM genes by the eukaryotic fungi compared to their prokaryotic counterparts, where some SM genes are only expressed in the presence of appropriate environmental signals. Research is currently going on to uncover new methods to activate these "silent" gene clusters. However, at the same time, continuously expanding our understanding of the relationship between SM compounds, the biosynthetic genes and microbial ecology will assists us in navigating the exponentially expanding seas of genomic information in the search for new bioactive compounds. The past four years, I have been involved in the elucidation of the SM pathways for viridicatumtoxin, griseofulvin, tryptoquialanine, cytochalasins, lovastatins, echinocandin, fumagilin and azaphilones. A specific example is given here on how the investigation into the genes and enzymes involved in the biosynthesis of an interesting molecule, viridicatumtoxin, eventually leads to the discovery of a new immunosuppressive compound, neosartoricin, from the human pathogens Aspergillus fumigatus and Neosartorya fischeri.

JAMS celebrated July at the Australian Museum with a diverse series of talks and food and drinks, kindly supported by ASM.

Rita Rapa (UTS) started us off describing the integron/gene cassette system in the Vibrio genus. These gene cassettes add to the adaptive potential of Vibrio and are likely to be an important driver in the evolution of Vibrio in their respective niches. Through whole cell proteomic analysis, deletions in the gene cassette array exhibit altered surface associated structures. Her future work will focus on how these deletions impact Vibrio physiology.
Event Date: 
Wednesday, July 27, 2011 - 18:00 - 18:15
Institution: 
UTS
Title: 

Gene Cassette Products and Their Role in Vibrio Physiology: A Proteomics Approach

Abstract: 

Vibrios are marine bacteria that are highly adaptable and subsequently capable of colonizing various niches. The integron/gene cassette system is a genetic element present in Vibrio spp., that incorporates mobile genes termed gene cassettes into a reserved genetic site via site-specific recombination. The integron consists of three basic elements: an integrase gene (IntI), an attachment site (attI) and a promoter (Pc). Gene cassettes contain an open reading frame and an IntI-identifiable recombination site called attC. Insertion (and excision) of gene cassettes is facilitated by an integrase-mediated recombination between attI and attC where cassettes can be accumulated forming a cassette array. Cassette arrays in Vibrio spp. are uniquely large, containing hundreds of contiguous gene cassettes. There is a consensus that these gene cassettes add to the adaptive potential of vibrios and have likely been an important driver in the evolution of vibrios into their respective niches. How this is achieved has been difficult to understand since 80% of gene cassettes are novel and consequently of unknown physiological function. Whole cell proteomic analysis comparing wild-type Vibrio rotiferianus DAT722 with isogenic mutants that have deletions in regions of their gene cassette array show the deletions have altered surface associated structures including extracellular polysaccharide and outer membrane proteins/porins. Studies into how the deletions impact the secretome/surfaceome are currently underway. This data aims to understand how the integron/gene cassette system drives Vibrio evolution by determining how these unique genes impact vibrio physiology.

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