Musings on a meeting of Australasian plant pathologists

In November 2019 I was excited to attend the Australasian Plant Pathology Society’s biennial conference in Melbourne. A big drawcard for me were the fantastic plenaries and keynotes spread across all three days of the conference. To start off Brett Summerell, the APPS President, showed us how we can effectively communicate scientific findings in a ‘post-truth, post-trust, post-expert world’ where facts are outweighed by opinion. Sophien Kamoun gave the EMBO Keynote lecture where he stressed the importance of sequencing and releasing the genomes of emerging plant pathogens, the new modes we have for releasing information and the impact that worldwide collaboration and free flow of information can have on a disease outbreak. There were also amazing plenaries by Carolee Bull on translational taxonomy, George Sundin on the fire blight pathogen, Thierry Candresse on viral detection with high throughput sequencing, Hailing Jin on small RNAs in plant-pathogen interactions and Neena Mitter on the development of an RNA spray for crop protection. I could go on and on!

There were so many interesting sounding talks across the five parallel sessions – I really wanted to have a Hogwarts time-turner so I could manage to be in multiple places at once! In the end I decided to concentrate my attention on the Biocontrol, Plant-Microbe Interactions and Pathogenomics sessions. These topics complement my PhD work where I’m using a genome-wide methodology to identify plant colonisation genes of a biocontrol bacteria. There were so many fascinating talks – some of the highlights that pushed me to the edge of my knowledge were on fungal genome sequencing, small RNAs and fungal effectors.

The three poster sessions were really busy! I enjoyed seeing a broad cross-section of plant science and meeting so many great scientists. The poster sessions gave me a peek into research areas where I didn’t get to see presentations and gave me lots of fantastic ideas for poster designs and the ways people use posters to communicate their science. It was wonderful to see both early career researchers and more senior members of the community presenting posters. I haven’t seen this broad range of career stages presenting posters at other conferences. This was a really great way to approach more senior scientists.

As well as attending the main conference I really enjoyed participating in two of the satellite sessions. The 4th Australian Pathogen Bioinformatic Symposium (APBS) was held at Agribio, La Trobe University the day before the main conference. I presented my work on transposon insertion sequencing in a plant-associated bacteria and had some great interactions with the researchers in the audience. It was a low-key, collegial start to the conference which meant I already knew a few people when I got to the much bigger main conference. Afterwards I enjoyed the Molecular Plant-Microbe Interactions joint session with the Australian Society of Plant Scientists, again at AgriBio. There were some really engaging presentations on topics as diverse as engineering the root microbiome with plant root exudates, detecting compounds on the surface of pathogenic fungi, and the transport of iron in Rhizobia-legume symbiosis.

To round out a wonderful conference experience there were two fabulous social events. The welcome reception was held the evening before the first full day of the conference and was a superb way to meet new people (plus the food was amazing!). The gala dinner was a more formal affair held in the stunning Mural Hall. I met a wonderful range of researchers over dinner and was introduced to some people I wouldn’t have met otherwise.

I’m very grateful for the support of APPS which allowed me to attend the conference, present my PhD research and meet so many fantastic scientists. Thank-you as well to the organising committee for supporting gender equality and making sure that there was gender balance in the presenters at every level.

Day in the life of a PhD candidate

7:30am Read through notes prepared by my project team to make sure I’m up to speed for this morning’s meeting. Contemplate the lack of suitable clothes in my cupboard and make a mental note to do clothes washing on the weekend.

8:30am Drive to campus. Realise there’s not enough time to get breakfast before my first meeting. Scrounge around in the car to see if there’s anything to eat. Come up with nothing.

9:10am Print notes so I can refer to them during the meeting. Print one-sided even though it’s using more paper, but I want to stick them in my lab book later as a record of what we discussed.

9:15am Pre-meeting with the team on campus to prepare for the Skype meeting with our collaborators. Spend most of the meeting trying to work out if my really busy supervisor is going to attend the meeting (spoiler alert: he didn’t make it).

9:30am  Skype for 2 hours with international and Australian collaborators. First 10 minutes is spent with everyone around the world trying to figure out the updated Skype program that isn’t intuitive. Discuss upcoming experiments with collaborators who have been working in the field for 30 years, make sure there’s nothing silly in our plans. Share the data I’ve generated and talk about the approach we’re taking for the next steps in the project. Collaborators express interest in our results, lament their lack of time to work through it and pronounce that they love doing science vicariously through us.

11:30am Debrief about Skype meeting and the next steps for experimental work and data analysis. Agree with co-supervisor that we’ll still go ahead with what we planned despite some potential problems. We won’t know if those things are problems until we’ve done the experiment and we’ve got a plan for how to identify them if they do occur, so we feel okay about it.

11:45am Get supervisor’s signature on reimbursement paperwork for conference attendance costs and discuss what funding should I use when purchasing a DNA extraction kit for my project.

11:54am Contemplate skipping the upcoming seminar to get lunch seeing I didn’t manage to have breakfast.

11:56am Colleague asks me if I want to walk to the seminar with her and that decides for me that I’m going to the seminar.




Notes from the departmental seminar.

12:00pm Seminar hosted by my department – Nature Communications editor discussing his career path from PhD to Post Doc to journal editor, what his job looks like on a daily basis and the editing process for manuscripts submitted in his area. Interesting to hear about what happens at an editorial desk and leaves me feeling like being a journal editor involves too much reading of the scientific literature.

1:00pm Finally get to have some food! Lunch at the campus hub and catch up on a TV show I didn’t get to watch last week. Friends turn up unexpectedly, so stop watching the show and discuss the pros and cons of the latest figure he created in R for a manuscript he’s writing.

2:30pm Pick up purchases from the science store on campus, attach their inventory barcodes and put them away in the fridge/freezer/cupboard in the lab. Update the lab whiteboard to show what is still to be delivered.

2:55pm Remember that I’ve hardly drunk any water today and fill up water bottle on my way to my next meeting.

3:00pm Attend R Users Group meeting on campus and learn about using base R functions instead of downloading an R package (this makes the code more accessible for anyone to use and future-proof as packages can change without your knowledge). Code along with the presenter and feel proud that I can keep up and understand what he’s doing. A knowledgeable guy in the front of the room is asking questions that make me feel out of my depth. Correct the balance by asking the presenter about base R resources for learners.

RStudio screenshot

R code from code-along session in R Users Group meeting.

4:15pm Take reimbursement paperwork to departmental admin staff for checking and processing before the end of year deadline. Answer emails and make sure I’ve dealt with all the budget/invoice emails before the end of year deadline tomorrow.

4:45pm Read some more of the super complicated paper I’ve been working my way through. Highlight some relevant passages. Get frustrated and give up.

5:00pm Discuss experimental plans for next week with a colleague and agree on a date that he’ll have some materials ready for me to preserve some cells for microscopy.  Clarify what I’ll need to do. Lament the fact that even though I’ve been doing useful/necessary things all day I don’t feel like I’ve achieved anything.

5:30pm Order DNA extraction kit using the university’s online ordering system. Marvel at how much better this is than the old paper-based system.

5:45pm Stick notes from this morning’s Skype meeting into my lab book so I can refer to them when planning my next experiments.

6:00pm Check Twitter notifications for my personal account and the lab account that I run. Re-tweet some interesting things from both accounts. Get lost in an internet rabbit hole. Realising I’m hungry makes me stop and pack up.

7:00pm Head out for the night and make my way to the local shopping centre for some Christmas shopping and dinner. Thank goodness that I have a shopping plan and realise that I could finish all my shopping before it’s even December. Yay for those transferrable PhD skills!