Clinical pathology

Event Date: 
Wednesday, February 27, 2013 - 16:15 - 16:45
Institution: 
California Institute of Technology
Title: 

Bridging the gap between ‘omics generated hypotheses and metabolic function of microorganisms in the environment.

Abstract: 

Rapid advancements in environmental ‘omics approaches (e.g. metagenomics, transcriptomics, proteomics) have provided a fresh perspective on the metabolic potential of uncultured microorganisms in nature.  However, our ability to directly test hypotheses regarding the ecophysiology of microorganisms in their natural environment remains a challenge.  New applications of whole cell fluorescence microscopy, stable isotope tracers and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS), provide direct cell-specific isotopic, elemental and phylogenetic information on the metabolic roles of environmental microorganisms and microbial associations.   This presentation will introduce the FISH-nanoSIMS method and highlight its utility for the field of microbial ecology through a case study of uncultured methane-consuming archaeal-bacterial symbioses in deep-sea sediments.

JAMS REPORT
Ani Penesyan
 
On the last Wednesday of spring we were spoiled with the room on the top floor of the Australian Museum and magnificent views of Sydney, yes, once again! Joining us were not only our regular JAMS crowd, but also visitors from Europe (yes, that is really cold in Europe during this time of the year!)
 

Event Date: 
Wednesday, February 27, 2013 - 18:30 - 19:00
Institution: 
University of Queensland
Title: 

The Big Picture: lessons from a rapidly expanding genomic tree of life.

Abstract: 

Most microorganisms cannot be grown in pure culture (or at least not easily). This has been apparent for decades by comparing the number of cells seen under a microscope to the fraction of those cells that will grow into colony forming units (typically <1%). The advent of culture-independent rRNA-based molecular surveys pioneered by Norman Pace put our degree of ignorance of the microbial world into perspective: dozens of major microbial lineages have emerged over the last 20 years that lack even a single cultured representative. New approaches, such as deep metagenomics and single cell genomics, are now transforming the rRNA-based phylogenetic outlines of the tree of life into a fully fledged genome-based view of the tree. I will present a snapshot overview of the genome tree of the bacterial and archaeal domains and examples of functional insights in the context of a more complete view of microbial evolution.

Event Date: 
Wednesday, September 26, 2012 - 18:15
Institution: 
Macquarie University
Title: 

Defining the effluxome of Acinetobacter baumannii

Abstract: 

 
Acinetobacter baumannii is a Gram-negative opportunistic human pathogen known to cause a range of infections in hospitals. Despite their recent emergence, strains of A. baumannii, resistant to essentially all routinely used antibiotics, have been isolated from clinical settings. Bioinformatic analysis identified more than 50 transporter systems with a putative role in drug efflux in the genome of A. baumannii ATCC17978, representing ~2% of all its protein coding ORFs. Based on an assumption that drug transport is often associated with over-expression of a relevant efflux system in the presence of the substrate, high-throughput quantitative reverse-transcriptase PCR (qRT-PCR) has been performed after shock treatments with sub-inhibitory concentrations of antibiotics and differential expression of genes was assessed. This strategy has led to the discovery of novel drug efflux systems and defined physiological functions for previously characterised and novel pumps in drug resistance.
Efflux systems have evolved for millions of years before bacteria such as A. baumannii entered the hospital environment. Presumably, they have initially developed as mechanisms of resistance against naturally occurring substrates. To further characterize the role of efflux systems, cultures of A. baumannii were treated with bioactive natural compounds found in the environment, i.e. soil. These treatments resulted in significant changes in the transcription of efflux pumps indicating their possible role in the defence against compounds found in nature.
Increased expression of efflux systems was also observed when cells of A. baumannii were grown in biofilms compared to planktonic cultures which could suggest that efflux pumps may also play an important role in the functioning of these bacterial communities.

 

Event Date: 
Wednesday, August 29, 2012 - 18:15 - 18:30
Institution: 
University of Sydney
Title: 

What is the substrate of the sMMO-like genes of Mycobacterium strain NBB4?

Abstract: 

Monooxygenase (MO) enzymes are important for biogeochemistry, biocatalysis and bioremediation. In microbes, MOs are best known as the catalysts for methane oxidation, which is a process of immense importance for the global carbon cycle and for influencing climate change. Mycobacterium strain NBB4, an ethene-oxidising isolate from estuarine sediment, contains a diverse array of MO genes, including homologs of the particulate and soluble methane MOs (pMMO/sMMO), cytochrome p450's, and an ethene MO. We have previously shown that NBB4 can biodegrade several chlorinated pollutants, and that the pMMO homolog is actually an ethane/propane/butane MO. The function of the sMMO homolog in NBB4 (genes designated smoXYBCZ) is currently unknown. This gene cluster has only low identity to sMMO, and methane is not a substrate for growth of NBB4. The aim of this Honours project is to identify the substrate of this novel MO via knockout and heterologous expression experiments. Our hypothesis is that smoXYBCZ acts in the second step of the butane oxidation pathway to convert butanol to butanediol.

Event Date: 
Wednesday, May 30, 2012 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Deep sequencing of evolving populations in bacterial biofilms

Abstract: 

 

Bacterial communities growing as biofilms are subject to a distinct lifecyle, featuring initial surface attachment, microcolony formation and dispersal of cells. Bacterial biofilms are sometimes characterised by high levels of heritable phenotypic variants, presumably resulting from genetic diversification during the biofilm lifecyle. As biofilms are a favoured lifestyle of many environmental and pathogenic bacteria, identifying the evolutionary processes responsible for this diversification has important implications, both for our understanding of ecological processes, such as niche adaptation, and to clinically relevant questions, such as the evolution of antibiotic resistance.
I've used longitudinal genome-wide deep sequencing to reveal the underlying genetic structure of bacterial populations growing as biofilms, for the model organisms Phaeobacter gallaeciensis 2.10 (an abundant marine bacterium) and Pseudomonas aeruginosa 18A (a clinical Cystic Fibrosis isolate). Biofilms were grown under defined laboratory conditions known to generate reproducible phenotypic diversification. Samples from different stages of biofilm development were then sequenced to very high coverage (>800x). By accounting for sequencing errors using a matched-sample approach, variants with population frequencies as low as 0.5% could be accurately identified.
In general, the extent and nature of genetic variation was comparable for biofilms of both model organisms, being driven by selection for a small number of non-synonymous variants within key genes involved in biofilm- and competition-related pathways. These results also demonstrate that genome-wide deep sequencing can rapidly, accurately and comprehensively describe genetic variation within evolving populations.

 

Event Date: 
Tuesday, April 24, 2012 - 19:15 - 20:00
Institution: 
Nanyang Technological University, Singapore / UNSW
Title: 

The Great Escape: Biofilm formation and dispersal

Abstract: 

Bacteria form biofilms on almost all surfaces, ranging from ship hulls to cooling towers, to indwelling biomedical devices.  Biofilms also play positive roles, for example, floc and granule formation for the biological remediation of contaminated water.  Therefore, there is strong drive to understand the processes of biofilm formation, to either eliminate biofilm formation in some industrial processes and human health, or to encourage their formation, for processes such as remediation.  To develop innovative, environmentally friendly, biofilm control technologies, it is essential to understand the process of biofilm formation and how bacteria control the process of dispersal. 
Bacteria rapidly respond to changes in nutrient conditions, and we have shown that depletion of nutrients, e.g. carbon limitation or nitrogen, can lead to dispersal of bacterial biofilms.  This process is mediated via an intracellular second messenger cascade, using cAMP and c-di-GMP and may also be linked to other physiological signals such as nitric oxide mediated dispersal. 
We have also shown that biofilm development and dispersal is dependent on a prophage carried by Pseudomonas aeruginosa.  The phage plays an important role in multiple aspects of biofilm development and stability and we are beginning to unravel the mechanisms result in phage conversion which ultimately are linked to biofilm development.

Sydney may have failed to deliver some sunshine on the last day of a slightly extended summer, but this didn’t dampen the spirits of Sydney’s microbiology community who turned out in numbers for the Inaugural JAMS Anniversary half-day meeting at the Australian Museum. This special meeting celebrated the first birthday of JAMS, an ASM special interest group that aims to bring together research microbiologists, post-docs and PhD students working in non-clinical research from all institutes.

Special thanks must go to the sponsors of the meeting: POCD scientific; Becton, Dickinson and Company; Macquarie University; The University of Sydney; The University of NSW; The University of Technology, Sydney, and; The University of Western Sydney. Another special thank you must also go to Federico Lauro (UNSW) and other members of the JAMS steering committee for organising the anniversary meeting and for their continued commitment to JAMS. The steering committee would also like to thank the Australian Museum who kindly provided the venue for our regular meetings and who hosted this special event.

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