Biology

Event Date: 
Wednesday, November 26, 2014 - 18:00 - 18:15
Institution: 
UWS
Title: 

Clues of sexual reproduction in the Arbuscular Mycorrhizal Fungi: a putatively ancient asexual land-plant symbiont

Abstract: 

Arbuscular Mycorrhizal Fungi (AMF) are an ancient group of obligate land-plant symbionts which form a mutualistic symbiosis with the roots of over 80% of land plants  and are found in the majority of terrestrial ecosystems. The filamentous hyphae of these fungi grow throughout the soil, scavanging for water and nutrients and transfer these to the plant in exchange for plant produced sugars.  As a result, extensive underground networks can form where multiple fungal individuals can be connected to a single plant and a single fungus can be connected to multiple plants simultaneously.  AMF do not have cells, rather nuclei flow freely through a common cytoplasm and genetically distinct individuals of a species are capable of anastomosis – or hyphal fusion – where cytoplasmic and nuclear exchange may occur. Curiously, these fungi have been once classified as ‘ancient asexuals’ due the lack of any observable sexual structures and an assumed purely clonal life-style. I present recent insights from the genome of the model AMFRhizophagus irregularis which contains evidence of a genetic tool kit which looks more like that of a sexually reproducing organism. I highlight the extreme expansion of a group of MATA-HMG genes which normally act as master- regulators of sex in fungi and present insights into the structure and function of these genes from a survey of local and global populations of R. irregularis individuals along with transcriptional evidence via QRT-PCR that a subset of these genes have a functional involvement in AMF partner recognition and possibly sexual reproduction.

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 - 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.

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.
 
Event Date: 
Wednesday, September 24, 2014 - 19:15 - 19:45
Institution: 
Australian Centre for Ecogenomics
Title: 

Evolution and function of marsupial gut microbiota

Abstract: 

Despite growing interest in the form and function of mammalian gut microbiomes, few culture-independent studies have focused on the microbiomes of Australian marsupials. In particular, how do the microbiota of the koala and other toxic Eucalypt folivores enable these animals to occupy this specialised dietary niche? We are addressing this question by surveying the gut microbial communities of diprotodont marsupials across a range of phylogeny, diet, and gut morphology. Furthermore, beyond community profiles, we are probing community functionality through metagenome shotgun sequencing of the Vombatiformes (koala and wombat) gut microbiota. Using differential coverage binning and metabolic reconstruction, we have the comparative power to identify specialised pathways in koala and wombat microbiota, from the community-level down to the level of individual population genomes.

Event Date: 
Wednesday, September 24, 2014 - 19:00 - 19:15
Institution: 
CSIRO
Title: 

Animating the Gut Microbiome

Abstract: 

Animation can be a powerful way to inspire and educate people with science. Creating biomedical animations which depict advanced scientific concepts in a clear way requires 2 main considerations, 1) rigorous investigation of the underlying science, and 2) careful development of the story to express the ideas in a meaningful way.

In this talk Christopher Hammang will present his first biomedical animation “The Hungry Microbiome”. He will explore the challenges involved in animating the human gut microbiome and the unique insight gained from creating an animation about resistant starch. The talk will also explore the workflow and technology which can be used to create these biomedical animations, as well as a brief review of the science underlying resistant starch research.

 

Event Date: 
Wednesday, September 24, 2014 - 18:15 - 18:30
Institution: 
University of Sydney
Title: 

Cathelicidins in the Tasmanian devil (Sarcophilus harrisii)

Abstract: 

Antimicrobial resistance is increasing, posing a threat to human and animal health. A lack of new antibiotics means alternatives such as antimicrobial peptides are urgently required. Antimicrobial peptides are a primitive component of the innate immune system. Cathelicidins are a predominant family within mammals, contributing to host immunity through antimicrobial and immunomodulatory functions. They have been studied extensively in eutherian mammals but marsupials are relatively unexplored. Marsupials give birth to altricial young which are immunologically naïve. During development the young are protected from infection by mechanisms such as cathelicidins within the pouch. This unique reproductive physiology has encouraged lineage specific expansion of the cathelicidin gene family within marsupials, resulting in numerous diverse peptides.
 
The Tasmanian devil (Sarcophilus harrisii) is the largest remaining carnivorous marsupial and is currently under threat from a contagious cancer, devil facial tumour disease (DFTD). Human and bovine cathelicidins exhibit anti-tumour activity against a number of cancers. Furthermore, studies in the tammar wallaby have revealed the potency of marsupial cathelicidins against multi-drug resistant bacteria. As such, release of the Tasmanian devil genome in 2012 provides new avenues in the search for cathelicidins with the therapeutic potential to treat DFTD and resistant pathogens.
 
We identified 7 cathelicidins in the Tasmanian devil genome which were highly variable and distantly related to eutherian cathelicidins. Six Tasmanian devil cathelicidins have been synthesised and will be tested against a range of bacteria and fungi. Preliminary antifungal testing of two cathelicidins revealed that one peptide was more effective at killing Candida krusei, Candida parapsilosisCryptococcus gattii and Cryptococcus neoformans than the antifungal drug fluconazole. Cytotoxic and haemolytic activity of all six cathelicidins has also been determined. Four cathelicidins did not kill human lung epithelial cells or red blood cells, and only two showed moderate cytotoxic and haemolytic activity. This study highlights the potential for marsupials such as the Tasmanian devil to provide new drugs to treat human and animal disease.

Event Date: 
Wednesday, September 24, 2014 - 18:00 - 18:15
Institution: 
University of Sydney
Title: 

Microbiota characterisation in the Tasmanian devil

Abstract: 

The Tasmanian devil (Sarcophilus harrisii), the world’s largest remaining carnivorous marsupial, faces extinction due to the spread of a contagious cancer called Devil Facial Tumour Disease (DFTD). The lack of a description of the bacterial community composition in the species represents a major gap in our knowledge of Tasmanian devil biology. In this study we characterised 12 microbiomes from four body sites, including mouth, gut, skin and pouch, in five Tasmanian devils via PCR amplification of 16S rRNA gene V1-V3 regions followed by 454 sequencing.  A total of 249,224 reads with an average sequence length of 489 bp were obtained after length and quality filtering. The reads further clustered into 14533 operational taxonomic units (OTUs; sequence identity cutoff of >97%) that were classified to 24 phyla spanning 275 families. Higher levels of bacterial species richness were observed in the pouch and skin than in the mouth and gut. The pouch and skin showed similar microflora compositions, which may vary between animals, possibly due to different environments. Distinct from the previously reported koala gut microbiota [1], which is dominated by Bacteroidetes and Firmicutes, the devil gut microbiota was found to be dominated by Fusobacteria, Firmicutes and Proteobacteria, comprising up to 73.7-94.3% of the community. This study has greatly improved our understanding of the microbial communities in the Tasmanian devil, which will significantly contribute to the effort to conserve the species.

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