October 2014

Event Date: 
Thursday, October 9, 2014 - 16:00 - 17:00

Dear All,

 

You are invited to the Sydney Next Generation Sequencing Special Interest Group Meeting,  which will be held at the University of Technology, Sydney.

 

Further details are below:

 

Speakers: 

Event Date: 
Wednesday, October 29, 2014 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Ammonia-oxidizing bacteria play redundant roles with ammonia-oxidizing archeae in acidic soil

Abstract: 

 
It is widely accepted that ammonia-oxidizing achaea (AOA) dominates ammonia oxidization, the rate-limiting step in the nitrification process, in acidic soils, but their counterpart ammonia-oxidizing bacteria (AOB) which are ubiquitous in acidic soils should not be neglected. Researches about the functions of AOB in acidic soils are very few. Here, we investigated the abundance and community of AOA and AOB in acidic soils (pH 3.35 ~ 4.46) with nine different treatments (Ctrol, N, NK, NP, NPK, N+CaO, NK+CaO, NP+CaO, NPK+CaO) and found that significant positive correlations between potential nitrification rate (PNR) with the total amoA gene copy numbers of AOA and AOB. The community of AOB but not of AOA responded to CaO significantly. Moreover, microcosms incubation with different concentration CaO (N+0, 500, 1000, 2000 ppm CaO, pH 3.42 ~ 4.37) showed that the abundance of AOB amoA gene significantly increased in N+1000 and N+2000 treatments at day 7 while the abundance of AOA amoA gene significantly increased in N and N+500 treatments at day 60. The community of AOA and AOB changed significantly during the incubation. Phylogenetic analysis of bacterial and archaeal amoA gene in treatment N+1000 revealed that AOA belonged to group 1.1a-associated increased whereas that belonged to group 1.1b decreased significantly during the incubation.  AOB belonged to Cluster 10 increased significantly at day 7 but decreased during the last incubation while AOB belonged to Cluster 3a.1 and 3a.2 showed reverse trends during the incubation. Additionally, AOB belonged to Cluster 7 were obligately observed at day 7. Moreover, we studied the activity of ammonia oxidizers in treatments N, N+1000 and N+CaO with 13CO2-DNA-stable isotope probing incubation for 30 days. Interestingly, 13C-labeled carbon source was significantly assimilated into the amoA gene of AOB but not AOA at day 7 and the reverse result was observed at day 30 in treatment N+1000 though it was acidic soil. Significant assimilation of 13C-labeled carbon source was detected in AOA amoA gene in treatments N and N+CaO during the incubation. Taken together, these results suggested that AOB responded to the disturbance significantly then drove the ammonia oxidization in acidic soils, meaning that AOB played redundant roles with AOA in acidic soils though the two groups of ammonia oxidizers had special niches.

Event Date: 
Wednesday, October 29, 2014 - 18:15 - 18:30
Institution: 
UTS
Title: 

Stigmergic social behaviours facilitate the active expansion of Pseudomonas aeruginosa interstitial biofilms.

Abstract: 

Erin S. Gloag1, Awais Javed2, Huabin Wang3, Michelle L. Gee3, Scott A. Wade2, Lynne Turnbull1, Cynthia B. Whitchurch1*
1 The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
2 Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
3 School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia.
 
Biofilms are often found associated with infections of implantable medical devices; accounting for approximately half of all nosocomial infections. Biofilms are often thought of as sessile surface-attached communities that are embedded in a protective slimy matrix. However, many bacterial pathogens also have the capacity to actively expand their biofilm communities via complex multi-cellular behaviours. We have observed that when P. aeruginosa is cultured at the interstitial surface between a coverslip and solidified nutrient media the resulting biofilm actively expands via twitching motility and is characterised by the formation of an extensive pattern of interconnected trails.
We set out to identify the factors governing pattern formation and coordinated movement during P. aeruginosa interstitial biofilm expansion. Our observations have revealed that during biofilm migration the cells at the advancing edge create furrows as they migrate across the semi-solid media The following cells are preferentially confined to these furrows, resulting in the emergence of an interconnected furrow network and the subsequent extensive large scale-patterning characteristic of these biofilms.
Stigmergy is a concept which describes self-organisation processes observed in higher organisms and abiotic systems through indirect communication via persistent cues in the environment left by individuals that influence the behavior of other individuals of the group at a later point in time. Our observations indicate that self-organised pattern formation in P. aeruginosa interstitial biofilms is also a stigmergic phenomenon. To our knowledge this is the first time that stigmergy has been identified as a mechanism of self-organisation of bacterial biofilms and propose that the concept of stigmergy can be included in the repertoire of systems used by bacteria to co-ordinate complex multicellular behaviours. We are currently exploring the development of novel antimicrobial strategies aimed at controlling and inhibiting biofilm expansion in medical settings via exploiting our new understanding of biofilm expansion.

Event Date: 
Wednesday, October 29, 2014 - 19:00 - 19:30
Institution: 
UTS
Title: 

“On the value of reframing antibiotic resistance as a disaster risk problem”

Abstract: 

Dr. Maurizio Labbate1,2 & A/Prof. Dale Dominey-Howes3

1School of Medical and Molecular Biosciences, University of Technology, Sydney, Australia.
2The ithree Institute, University of Technology, Sydney, Australia.
3Asia – Pacific Natural Hazards Research Group, School of Geosciences, University of Sydney, Australia.

Abstract:

On the 1st May 2014 the World Health Organization in its first global assessment of antimicrobial resistance reported that antibiotic resistance has now reached alarming proportions and is no longer a future problem but a contemporary reality. This comes off the back of other urgent calls from leading authorities including the Deputy Director of the Center for Disease Control (CDC) who has publicly stated that we have now reached the “end of the antibiotic era” and the UK Chief Medical Officer, Professor Dame Sally Davies who called for antibiotic resistance to be placed on the risk register above the issue of terrorism. Increasingly, the tone of the language used by these organizations and individuals is reminiscent of that used by the disaster and emergency risk management communities to describe commonly occurring disasters such as earthquakes, fires, floods and storms.

Antibiotic resistant infections are rising fast and affect millions of people globally. Antibiotic resistance has become a slow onset disaster that like climate change has struggled to elicit the sort of coordinated international response that is required to deal with the magnitude of the emergency. Anthropogenic modification of the Earth’s climate system provides the foundation for sudden onset natural disasters such as hurricanes, wildfires and storms. Likewise, increasingly widespread antibiotic resistance is laying the foundation for the future occurrence of sudden onset bacterial epidemic and pandemic disasters.

Despite the finest efforts by medical and health policy makers and communities to control the antibiotic resistance problem, the issue has reached a critical tipping point. Given the current state of the antibiotic resistance problem and the likely near future of untreatable bacterial infections, we propose an alternative and novel policy perspective. With this is mind, we propose to make antibiotic a broader issue and reframe it as a disaster risk problem and engage the expertise of emergency managers. Governments and disaster policy makers across the world use the Emergency Risk Management process in the management of and preparation for natural disasters. This process is a systematic method that through engagement with multiple stakeholders identifies, analyses, evaluates and treats risks and takes an iterative approach with well-defined activities that lead to implementation of risk-treatment strategies tailored to a specific community’s risk profile. This policy and practice framework is an excellent mechanism for reaching out to communities and communicating complex messages – an area that needs to be enhanced.

You are invited to the Sydney Next Generation Sequencing Special Interest Group Meeting,  which will be held at the University of Technology, Sydney.
 
Speakers: 
A/Prof Aaron Darling (ithree Institute, UTS), MinIONs & Hi-C: short vignettes on the state of nanopore sequencing and application of Hi-C to metagenomic sequencing. 
Dr Fabian Buske (Garvan Institute of Medical Research), Title to be advised.
 
When: Thursday 9th October, 4.00pm – 5.00pm followed by drinks and nibbles. 
Where: Room 5.01, Level 5, Building 4, University of Technology, Sydney.