Zoe's mini-interviews with eight Australian ECR and PhD researchers!

Posted by on 5 September 2015 | Comments

Hi everyone!

Coming towards the end of my role as your ASM Communications ambassador for the last two weeks I thought I would like to share some mini-interviews I've been very fortunate to conduct with talented early career and postgraduate researchers located throughout Australia at both regional and metropolitan campuses/institutes. Their projects are fascinating and they're all at different stages in their work in the areas of wastewater microbiology, virology, bioinformatics, environmental microbiology and more!

I hope you find their interviews and projects as interesting as I have!

Warm regards,

Zoe.


Mini-interview: Lachlan B. M. Speirs

PhD Candidate, La Trobe Institute of Molecular Sciences, La Trobe University, Bendigo Campus

What are you currently researching and how? I study several filamentous bacteria that cause wastewater treatment processes to fail. The particular organisms I am studying were previously unidentified, and now we see they predominantly belong to the phylum Chloroflexi. Previously I have used Fluorescence In Situ Hybridization (FISH), Microautoradiography, Clone libraries, PCR (of course), and Sanger sequencing. More recently we have moved in to next gen sequencing and utilizing software to achieve some of our goals.

What drew you to this project/area? I have always been interested in environmental conservation, biology and engineering. Biotechnology, and particularly wastewater treatment, is very important to the environment due the need to remove pollutants and recycle water. I believe water is the most important commodity in this region.

What interests you the most? Originally I was most interested in discovering the identity of those bacteria filamentous causing problems in wastewater treatment plants. Now I find that investigating new strategies, often using the newer technologies, to better and/or more efficiently study microbial communities is very exciting.


Mini-interview: Imogen Bermingham

PhD Candidate, University of Queensland

What are you currently researching and how? I work on RSV (Respiratory Syncytial Virus), a leading cause of paediatric pneumonia and bronchiolitis worldwide. More specifically, I am interested in membrane fusion and teasing apart the steps of the viral entry process. RSV binds to the surface of cells and then initiates fusion of the viral and cell membranes through its fusion protein, F, which is the major focus of my PhD. I employ a lot of site-directed mutagenesis to probe residues and domains important in different steps of the entry pathway. RSV F is somewhat unique amongst the Paramyxivoridae in that the fusion protein can initiate fusion without the need for other viral proteins, so F mutants can be easily assayed in tissue culture by transient transfection of a codon optimized plasmid. I’ve been using a combination of Western blot, flow cytometry and tissue culture-based fusion assays to assess the many mutants I’ve generated. I also do recombinant protein work expressing particular host proteins and assessing their role in the entry process through classic PRNTs and binding assays.

What drew you to this project/area? Initially I was interested in virology and didn’t particularly mind what kind of project I was involved in – I just wanted to work with viruses! As any virologist will attest, they’re incredibly elegant and fine-tuned to do what they do and being able to study any aspect of that was exciting for me. Now, I really enjoy studying entry, the first step in the virus replication cycle, and it’s exciting thinking of ways to understand the process so we can stop an infection before it even starts. I started my project as an Honour student and really enjoyed working at the bench doing basic virology and was part of a really great team with excellent supervisors, so that encouraged me to stay.

What interests you the most? I think the most interesting part of my work is seeing how such a small change can have such a large impact on a proteins’ function. It makes you really appreciate virus evolution. The F protein is in a really metastable state that transitions into an energetically favourable post-fusion form - RSV F keeps a really fine balance by staying unstable enough that it can readily trigger when it contacts its host cell, but not too unstable that it triggers prematurely and becomes non-infectious.


Mini-interview: Jen Wiltshire

PhD Candidate, La Trobe University, Bundoora Campus

What are you currently researching and how? My research interest is in understanding the ecology of soil microbial communities and the practical applications this information will have for global sustainability. In particular I am interested in the contribution that soil microbial communities can make to the plant-based-bioremediation of anthropogenic pollution (particularly heavy metals) and to sustainable agricultural practices. I collaborate with soil scientists, community ecologists and bioinformaticians and utilize community-based approaches including community finger-printing and next-generation sequencing technologies to understand the function of soil microbial communities in a variety of soil conditions. Ultimately I am interested in understanding how soil microbial communities promote plant growth and what drives them to do so. With this information we can utilize soil microbial communities to improve both agriculture and bioremediation.

What drew you to this project/area? I love the complexity of biological systems; Unravelling how they work is an exercise in investigative thinking and problem solving which I love. I’m also fascinated by the potential application of microbial communities in areas like agriculture and medicine. I think as the technology to investigate microbial communities continues to develop we will make some surprising and probably important discoveries indeed.

What interests you the most? The integration of knowledge from many disciplines: I work on microbial communities, but unravelling how they function as part of the ecosystem draws on knowledge from soil chemist, biochemists, ecologists, plant biologists and so many other fields that I can’t possibly become an expert in all of them. This means that I am constantly learning things from other researchers. When information from these different sources fits together to explain my data it is always super interesting, and I think elegant.


Mini-interview: Amir Mohamed Hassan

PhD Candidate, University of Western Australia

What are you currently researching and how? Currently, I'm building up on my preliminary bioinformatics identification of prophages in Moraxella catarrhalis, by indirectly visualising phage(-like) particles from an induce lysate of selected M. catarrhalis strains. The methodology has somewhat come full circle; I started off with the classical induction and testing for plaque identification (a gold standard for presence of inducible lysogenic prophages), but had no results, leading to the bioinformatics approach. After refining the range of lysogenic strains, I've attempted induction again, but this time stained the lysates with a fluorescent marker for DNA (SYBR Gold), and visualised the results with epifluorescent microscopy. The results are very promising, so far showing 3/3 strains with inducible phage-like particles, even though they could not produce plaques on various plaque assays, and under varying conditions. The next step is an isolation of the phage DNA from the lysates, and comparing the sequence to the prophage sequences identified via bioinformatics.

For the phenotypic assays, I'm using standard epifluorescent techniques. The stain I'm using is, as above, SYBR Gold, and the assays I've used are 1) a wet mount method, involving the preparation of samples on a microscope slide (with optional chemical flocculation beforehand), staining, anti-fade exposure, and visualisation, and 2) a filter mount method, where the sample is first filtered through a 0.02um Anodisc filter, followed by staining of the filter with possible trapped phages, and visualisation. The key step seems to be the concentration steps (because we believe even the artificial induced rate of these prophages is very low), which, in the wet mount method is via chemical flocculation with FeCl3, and in the filter mount method, with the anodisc.

In terms of bioinformatics tools, I've used quite an array of scripts and programs throughout, but the ones most relevant to (pro)phage detection and analysis would be PHAST, BRIG, EasyFig, Virfam, SPADES, Mauve, and MrBayes / MEGA 6.06

What drew you to this project/area? Initially I was interested in molecular microbiology, with the bulk of my exposure coming from the (mini) research projects I had conducted during my Natural Science degree, and the Masters of Infectious Diseases. However, due to some unfortunate luck with the phenotypic induction methods, I was referred to bioinformatics methods instead. Not having a computing background made this a really steep learning curve, that's how I got into it, and I'm pretty happy to have done it because the bioinformatics skills seem very transferable.

What interests you the most? I would say the most interesting part of the project/work is problem solving with new tools. Usually I'll encounter a problem which can't be solved with the current bioinformatics tools I have, and it's always interesting and humbling to find out that there's tools out there that do things in a more efficient and elegant way to solve those specific problems. Perhaps this is mostly to do with that I am not a bioinformatician (-ticist?) by training, and most things will seem novel as I expand my horizons, but I would think that science in general is structured this way around self-learning and discovery.


Mini-interview: Dr. Damien Finn

Postdoctoral researcher, University of Queensland

What are you currently researching and how? We are exploring the function and ecology of microorganisms involved in terrestrial biogeochemical cycling, primarily those involved in greenhouse gas production or consumption. To accomplish this, we use molecular biology tools such as transcriptomics to see biological function under given conditions, chemical analyses to observe environmental changes, such as gas chromatography and isotope ratio mass spectrometry, and mathematical modelling to demonstrate how the biology and the environmental chemistry are linked.

What drew you to this project/area? I have always been interested in all aspects of biology, from the great (I still have all of my Nat Geographic encyclopedias, Australia's Dangerous Creatures and dinosaur books from childhood) to the small (microbiology!). It wasn't until my undergraduate university years that I began to appreciate how our planet is more of a microbial planet than anything else, and that all planetary cycling and function that allows 'higher organisms' to exist is driven by an incredibly complex microbial engine.

What interests you the most? It's somewhat two-fold - I enjoy learning and applying new concepts, which is why biogeochemistry appeals to me, as it forces me to keep on top of a range of scientific disciplines. Secondly, my interest stems from the chance to get under the hood and see the what, the who and the why behind the ridiculously complex microbial engine that is so essential for running our planet as we know it.


Mini-interview: Ryan Wick

Research Assistant, University of Melbourne

What are you currently researching and how? I am currently developing a program, Bandage, which is a tool for visualising and working with assembly graphs. Bandage is coded in C++ using Qt. The assemblers I mainly use are SPAdes, MEGAHIT and Velvet. I use it to help my colleagues better understand bacterial isolate genomes as well as metagenomes.

What drew you to this project/area? I have an undergraduate degree in biology and have been a hobbyist programmer for a while. Before my Master's in bioinformatics, I had worked on some personal programming projects that never had many users in the real world. They were enjoyable, but I was keen to build something that people would actually use and appreciate. After studying bioinformatics, I realised that the field is often deficient in graphical programs which allow users to see their data in a user-friendly way. When I ran into a problem myself (analysing assembly graphs) that I couldn't solve without a good visualisation, I was inspired to create Bandage.

What interests you the most? I find software development very satisfying - it is fun to watch an idea materialise into a working program. I enjoy getting new feature requests from my users and turning them into a reality. And while it can be frustrating at times, tracking down and solving bugs can also be fun - it's like detective work!


Mini-interview: Lucy Furfaro

PhD Candidate, University of Western Australia

What are you currently researching and how? I’m currently researching Streptococcus agalactiae, also known as Group B Streptococcus (GBS), which can cause significant health issues for infants if they become infected. Transmission can occur vertically (from the mother to the child) during natural delivery from a colonised mother or even in utero, therefore pregnant women are generally screened for GBS during pregnancy. If the woman is found to be colonised they commonly receive antibiotics which not only eradicate the GBS, but also a range of commensal bacteria and can result in dysbiosis. With increasing knowledge of the importance of the microbiome, this broad spectrum approach is not an ideal approach. In addition, widespread prophylaxis of this nature is sure to increase the emergence of resistant organisms, further compacting the issue.

My PhD project aims to search for targeted alternatives to antibiotics, in particular bacteriophages. Bacteriophages are highly specific for their host bacteria and in this scenario present an attractive option. By screening 1000 Western Australian pregnant women, I aim to characterise GBS prevalence and screen for bacteriophages with activity against clinical GBS isolates.

I’m currently researching in the field of Women’s and Infants’ Health and more specifically the bacteria Streptococcus agalactiae, also known as Group B Streptococcus (GBS), which can cause significant health issues for infants if they become infected. I aim to identify lytic bacteriophages with activity against clinical GBS strains in the hope this could become a targeted non-antibiotic treatment in the future. My project involves culture and molecular analysis (multiplex real-time PCR) as well as transmission electron microscopy and whole genome sequencing.

What drew you to this project/area? I was drawn to this area because firstly, I love microbiology and secondly, I’ve always found the idea of phage therapy as an exciting prospect and would enjoy translating my work into a clinical setting.

What interests you the most? For me, I’m most interested in the whole process of discovery and trying to improve the health and wellbeing of mothers and their children.


Mini-interview: Matthew T. Doyle

PhD Candidate, University of Adelaide

What are you currently researching and how? I am just finishing up my PhD studies (Thesis submitted), and finishing off related experiments and some loose ends. I am interested in bacterial protein secretion systems of the Type V flavour (ieAutotransporters) because their secretion is extremely interesting mechanistically, and they are usually very important virulence factors produced by Gram-negative pathogens. Specifically, I’ve studied the biogenesis pathway of the essential autotransporter IcsA from Shigella flexneri. IcsA is a surface protein present on one pole of these rod shaped bacteria which initiates the creation of motile tails by hijacking the actin polymerising machinery of infected gut cells. I asked the questions; (1) how does IcsA get to the pole?, and (2) how does IcsA get to the cell surface? Happily, these questions resulted in three publications relating to the first question, and one relating to the second. One of my most interesting findings is that IcsA (and thousands of other autotransporters in many different pathogens) contains a previously uncharacterised conserved motif that allows (at least for IcsA) efficient secretion to the cell surface. We called this the PATR motif.

What drew you to this project/area? I began to be interested in bacteriology in general once I started to receive lectures from Associate Professor Renato Morona. Renato’s love of the science behind bacterial pathogenesis and bacterial cell physiology was infectious and I eventually dove into postgraduate research under his supervision. During my studies I became fascinated by protein secretion, principally autotransport. There is a particular beauty in the simplicity of this pathway that really draws me in. Yet, there are major unknowns and subtleties in this system that certainly intrigues me and challenges me intellectually.

I have found that very basic methods can be combined for great effect. I’ve used quantitative fluorescence microscopy as a staple in my studies. I’ve done this on both free Shigellae and in infected tissue culture models. Indeed, tissue culture models were quite useful in complementing results obtained in simple broth culture. For further looking at secretion, bacteria can be exposed to impermeable proteases (ie degradation indicates secretion and vice versa). This can be coupled with pulse-chase methods to get a temporal sense of the pathway. I’ve also employed very basic bioinformatics and data/metadata mining to help characterise the new autotransporter motif. With no background in bioinformatics, I found this particularly difficult but tremendously rewarding regarding results and understanding.

What interests you the most? I think it is interesting how answering a question generally leads to further questions (which are usually even more interesting). I’ve found this to be a constant so far. For instance, what is the specific function of the PATR motifs? I have shown that they are required for efficient IcsA secretion, but we are unsure of the molecular mechanism. Does the PATR directly enhance outer membrane translocation, or is it involved at an earlier/later stage of the pathway? Why do some autotransporters have PATR motifs, but others do not? These questions remain to be solved – but this is the exciting part!


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