Author Archives: Belinda Fabian

JAMS10: Day 2’s a journey through antibiotics, hot spring microbes, microbiome medicines, more nitrifiers, attachment, and scientific thinking

Posted on by

Day 2 of the JAMS10 Symposium started with Tim van Opijnen from Boston College giving us a whirlwind tour of his lab’s work on detecting antibiotic resistance mechanisms, using entropy as a predictor for an organism’s fate and the hundreds of ways tolerance can occur in an antibiotic specific manner. Next up was Dianne Newman from California Institute of Technology discussing the agathokakological (a mix of good and evil – love a vocab lesson to start a talk!) roles for redox active phenazine antibiotics produced by Pseudomonas aeruginosa. 

The first talks of JAMS10 day 2.

The third presentation in the session was Roland Hatzenpichler from Montana State University introducing us to metagenomic studies of archaea from Yellowstone Hot Springs, a relatively low complexity environment, to test hypotheses about organisms predicted to be methanogenic. The final speaker in this international session was Ashlee Earl from The Broad Institute of MIT and Harvard giving us insights into Enterococcus. Big props to Tim and Ashlee for planning ahead for the effects of a hurricane and pre-recording their talks!

Presentations on Yellowstone hot spring microbes and Enterococcus rounded out the morning session.

In the afternoon the second poster session was held along with a panel session on working outside academia. Four scientists with diverse positions came together to discuss their paths from their PhDs out of academia, how they picked up the necessary skills for their current roles and how much they rely on their technical training in their everyday work. It was inspiring to hear that some panellists didn’t know what they wanted to do, even at the stage of completing their PhDs, that non-linear career paths are normal and there can be plenty of successes and satisfaction on a non-traditional career path after a PhD.

A fascinating panel session on microbiology careers outside academia.

The afternoon international session started off with Samuel Forster from Monash University walking us through developing medicines using information from microbiomes, followed by Iruka Okeke from the University of Ibadan discussing adherence in E. coli, the exceptional bacterial coloniser of the digestive tract. Sebastian Lücker from Radboud University Nijmegen continued the conversation on nitrifying organisms and in situ detection of nitrifying microbes in complex samples.

The afternoon’s talks on E. coli attachment and nitrifying organisms.

These presentations were followed by Lone Gram from the Technical University of Denmark exploring why bacteria produce antibiotics and if they truly are secondary metabolites. The final speaker of this session was James Prosser from the University of Aberdeen who wrapped up the talks with a fascinating discussion (without any slides!) of scientific thinking in microbial ecology including inference, biased hypotheses based on arbitrary observations, assumptions and qualities of good hypotheses. Jim put forward the idea that it’s not technical challenges that limit progress in microbial ecology, but a lack of a scientific approach. 

Rounding out the symposium with two wonderful speakers.

The last task of the day was to wrap up the conference and announce the prize winners. Shang Yu Shueh was awarded the JAMS Community Advancement and Co-operation Award (the trophy is a toilet seat to recognise that the winner got sh*t done!). The wonderful support of the sponsors allowed for many poster presenters to be recognised for their hard work. Congratulations to all the winners!

Congratulations to all the prize and award winners!

Thanks to the JAMS10 organising committee for another excellent microbiology meeting and for creating a space for environmental and fundamental microbiology. The team of 45 pulled off an extremely professional event after pivoting from in-person to online with short notice. The only thing that was missing was the roar of applause at the end of a fabulous symposium! For more information visit jams.org.au or check out the #JAMS10 hashtag on Twitter.

The dead Jedis (two of the JAMS co-founders) wrapping up the JAMS10 Symposium.

JAMS10: SARS-CoV-2, fungal tree of life, halogenated pollutants, nitrifying microbes, symbionts and machine learning (and it’s only day 1!)

Posted on by

A new world needs a new way of conferencing and JAMS has taken full advantage of new technologies to make that happen. This year marks the 10th annual symposium of Joint Academic Microbiology Seminars (JAMS) so, despite the COVID-19 pandemic, the executive committee was determined to get everyone together to celebrate. 

A lightning tour of JAMS over the past 10 years.

New outbreaks around Australia and the world meant getting together in person was off the cards, so the team quickly pivoted to use GatherTown to create a custom online meeting place called JAMSTown. Every attendee makes an avatar that moves around the online conference space, and turning on microphones and cameras means attendees can chat and see each other in real time – it’s quick to set up and easy to get the hang of. There are plenary halls for the two streams, Sydney and Kuala Lumpur, a poster hall where attendees can chat with the poster presenters, places to chat and even a games room and beach! Zoom was used to bring together people from all around the world to talk about microbiology research.

JAMSTown main hall (left) and Exhibition Hall (middle & right) where attendees could chat with the sponsors about their research.

The online symposium opened up opportunities to attract big names in microbiology from around the world. The first joint session brought us three plenary speakers, two on SARS-CoV-2 detection on surfaces and in wastewater, and the third on mycology. Forest Rohwer from San Diego University gave us a whirlwind tour of sampling and using genomics to detect if SARS-CoV-2 virus was hanging out on commonly touched, rarely disinfected surfaces in San Diego, Janelle Thompson from Nanyang Technological University introduced us to wastewater surveillance for COVID-19 and Jonathon Plett from Western Sydney University explored the impact of genomic sequencing on mycologists’ understanding of the fungal tree of life.

Three speakers from the first international session of JAMS10.

The poster session in JAMSTown was a good analogue of an in-person poster session. The platform allows poster presenters and visitors within a small area to talk and see each other using their computer’s microphone and camera, so the interaction and Q&A part of a poster session is still possible. There were 57 posters submitted by JAMS attendees; that’s a lot of posters to visit in two poster sessions!

One of the two poster halls in JAMSTown – whole room view (left) and private space for each poster presenter to chat with attendees (right).

After a break, the JAMS founders panel discussed the development of JAMS in the 10 years since it’s foundation, their ideas for JAMS for the next 10 years (hand it over to the young ones!) and Australian microbiology. There’s always plenty of laughs when Federico Lauro, Mike Manefield, Ian Paulsen, Mike Kertesz and Andy Holmes get together. 

The JAMS Founders panel – in Zoom (left) and in JAMSTown (right).

In the second international session of the day, Jianzhong He from the National University of Singapore taught us about detoxifying halogenated organic pollutants and Mike Jetten from Radboud University Nijmegen introduced us to new anerobic microbes (‘spookmicrobes’) involved in the nitrogen and methane cycles. 

Mike Jetten (left) introduced us to ‘spook microbes’ and Jillian Petersen (right) took us on a 400 million year adventure.

In the second part of the session Jillian Petersen from the University of Vienna took us on a tour across 400 million years of microbial symbiosis with marine clams and Holger Daims from University of Vienna gave us insights into new discoveries in the ecology and function of nitrifying microbes. The final speaker of the session, Lauren Cowley from the University of Bath, taught us about machine learning for attributing locations for Salmonella enteritidis infections in the UK.

The professional setup of JAMS10 streaming through JAMSTown – speaker view (left) and a Q&A session (right).

Big thanks go out to all the JAMS10 sponsors! Without their support this online conference would not have been possible. Thanks to HelloBio for sponsoring a competition to win free tickets to JAMS10; I was very excited to be a winner! Overall an amazing day filled with a diversity of microbiology and speakers from across the globe – looking forward to a lot more microbiology on day 2 of JAMS10 tomorrow. For more information visit jams.org.au.

Why doesn’t the assignment operator shortcut work?

Posted on by

I’ve recently moved from exclusively using R scripts to incorporating RMarkdown files and came across (what I perceived as) a problem with the assignment operator shortcut.

I used the Mac shortcut of Option + – and RStudio gave me an equals sign (=) instead of the assignment operator (<-). I tried a bunch of other key combinations and managed to resize my RStudio display and get a bunch of other characters returned, but no assignment operator.

Source: Image by fancycrave1 from Pixabay 

Up to now I’ve only used R scripts, so I had a small panic about versions changing and new shortcuts (not sure why seeing I haven’t installed a new version). Then to Google!

Not many helpful options. Mostly links telling me the RStudio keyboard shortcut for the assignment operator (thanks, but I already know this) and other RStudio shortcuts.

After reading through the comments on a RStudio GitHub issue this comment gave me a lightbulb moment:

“In an R markdown document, do you by chance get = when composing text but <- within a code chunk?”

ronblum – https://github.com/rstudio/rstudio/issues/2486#issuecomment-663187110

I was trying to create an assignment operator in the text section of a markdown file so the shortcut wasn’t working. Tried out the shortcut in a code chunk and it’s fixed. That is to say, it was never broken – a case of operator error (ha!).

R coding and lots of Googling

Posted on by

I’ve been working in R long enough to have Googled the same things multiple times. It’s time to blog these things so they stick in my brain. Or failing that (let’s be honest!) I can look up my own blog.

I hope these linked posts help you learn about R coding or shortcut your frustration.

  1. Why doesn’t the assignment operator shortcut work?

Thanks to Jen Richmond, RLadies Sydney and the Macquarie Uni R Users Group for the idea and motivation to share thoughts on things that I stumble over so others can learn too.

Source: Image by 377053 from Pixabay 

Musings on a meeting of Australasian plant pathologists

Posted on by

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!

Sophien Khamoun presenting the EMBO Keynote lecture
Sophien Khamoun presenting the EMBO Keynote lecture
Lois Ransom presenting on the International Year of Plant Health
Lois Ransom presenting on the International Year of Plant Health
Brett Summerell, the APPS President, presenting on effective communication of science
Brett Summerell, the APPS President, presenting on effective communication of science

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.

IMG_9378
IMG_9367
IMG_9295

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.

15 tweets for a better conference experience

Posted on by

You (or your institution) paid a lot to go to a conference, so it only makes sense to maximise the experience. Here are 15 tweets you can send in the lead-up, during and after a conference to level up your conference experience and get everything you can from it.

For me, Twitter is an essential part of a great conference experience. I can connect with people I wouldn’t normally meet, I can get a glimpse into parallel sessions (I wish I had a time-turner like Hermione!*), I can share the conference with people who can’t be there and I can jog my memory afterwards.  All of this conference good-ness comes through the use of the conference hashtag.

To be able to connect with other conference attendees ALWAYS use the conference hashtag when tweeting. You might be super lucky and have people following your feed to see what’s happening at the conference, but that’s normally the exception, not the rule. The way strangers (both at the conference and at home) find your content is through the conference hashtag. If you don’t know the hashtag then check the conference organiser’s Twitter account or search the conference name on Twitter**.

Here are 15 prompts (with example tweets) to make the most of your next conference – everything from planning all the way through to the end of a conference:

1. Submitting an abstract – it’s likely that people in your field follow you so tweeting about submitting an abstract is a good way to create a conversation about the conference and encourage others to attend.

2. Registration – express your excitement about an upcoming conference, let people know you’ll be there and that you’re keen to meet up. I find starting conversations with strangers intimidating, so chatting on Twitter before conferences allows me to make connections online then continue them in person. This often saves me from the awkward beginning of a conversation as we can skip straight to something we already know we have in common.

3. Acceptance for a talk or poster – express your thanks to the organisers and advertise your presence at the conference. If people know you’ll be at a conference the greater the chance that they’ll come to your presentation.

4. Preparing your talk or poster – this is a good way to get advice from other attendees or clarify the requirements (I didn’t follow the hashtag rule here, oops!).

5. On your way to the conference – a chance meeting in an airport with another conference attendee means when you arrive you’ll already know someone.

https://twitter.com/VictoriaCarr_/status/1152926793193730053

6. Excited for the start of the conference – let people know you’ll be there and tweeting while at the same time re-affirming the conference hashtag.

7. Poster location and/or talk time – there a lot of things happening at conferences, so don’t be shy about spruiking your talk or poster – tag people who you think might be interested or invite specific people to come to your presentation.

8. Tips for conference attendees – share something that could improve the experience of other conference attendees. For example, I write my Twitter handle on my name badge so people can make the link between me in person and my profile online. Or once we’ve chatted they can look me up on Twitter.

9. Live tweet the talks – try to tweet at least once per talk or poster you attend, or more if you can manage it. The golden rule is DON’T tweet unpublished work! The presenter may ask for some slides or sections not to be tweeted or you might need to work it out for yourself. (Live-tweeting is a skill you can develop, there’s a follow-up post on this coming soon!)

10. Conference events that are coming up or you have attended e.g. ECR events, student events, booths to visit.

11. Fun things that are happening at the conference e.g. lucky door prizes, competition entries for talking to vendors, ice breakers, themed merchandise.

12. Photo of yourself or with a person you met at the conference – tiny Twitter profile photos can make it hard to see what someone looks like, use this tweet to circumvent that problem.

13. Prizes awarded at the conference – show your support for an award recipient or share your excitement about receiving a prize.

14. Thanks for coming to my talk/poster – this is a great way to get your research in front of more eyeballs; I try to re-tweet someone who tweeted about my talk or poster.

15. Thanks to the organisers for running the conference. This is a great way to wrap up a series of conference tweets and express your appreciation for all the hard work that goes into organising these events.

The order of these tweets is not set in stone. Some conferences may not have some of these steps, others may have aspects that I haven’t mentioned – adjust your tweets according to the specifics of your conference. If you’re interested in trying live-tweeting, then stay tuned for a follow-up post that goes into this in more detail.

My main conference tweeting tip is to get in early and often to keep yourself in the forefront of the attendee’s minds. And as always, include a picture (where possible) to increase the reach and engagement of your tweets!

Most of all, have fun and experiment with conference tweeting to make the most of your conference experience!

——

*Hermione is a character from the Harry Potter series who had a time-tuner which allowed her to travel through time and attend multiple classes that ran in parallel. ^

**The conference hashtag is usually set well in advance of the conference by the organisers, but if you can’t find one then get in touch with the conference organisers to suggest one ASAP. Highly likely they’ll be happy to put one in place as this is how people will find conference content. They don’t want people using multiple hashtags as this will dilute the impact. ^

JAMS symposium = microbiomes, antimicrobial resistance, halotolerant bacteria and picoplankton

Posted on by

On the 20th of March, microbiologists from all over Australia attended the 8th annual symposium of JAMS, the Joint Academic Microbiology Seminars, at the Australian Museum.  JAMS was very popular on Twitter, with many people live tweeting the talks (check out the #JAMS2019 hashtag).

New to JAMS this year was the live-stream of the talks. People all around Australia and the world (or just down the road) had the opportunity to be part of the event, even though they weren’t there in person. What a great way to increase access to microbiology and spread the word far and wide!

Microbiomes were a major topic of the day with talks on:

  • using microbial communities in conjunction with geochemistry to reduce iron in duricrust formation (by Emma Gagen from University of Queensland);
  • moving beyond data generation in microbial ecology and relating the large amount of data back to biological and ecological principles so we can successfully derive biological meaning from these datasets (by Andrew Holmes from Sydney University);
  • the importance and forecasted direction of microbial ecology (by James Tiedje from Michigan State University); and
  • the valuable work the Australian Microbiome Initiative is doing to create a resource of Australian microbial data for use in management, monitoring and R&D (presented by Sophie Mazard).

https://twitter.com/Sassihp/status/1108229128103186432

During the afternoon break we headed to the top floor of the Australian Museum for a poster and networking session. What a wonderful view and so many excellent posters and conversations!

Continuing the environmental microbiology theme there were also talks taking us through:

  • the history of oceanic picoplankton (by Daniel Vaulot from CNRS);
  • the role of wastewater in the transmission of antimicrobial resistance (by Erica Donner from Uni SA’s Future Industries Institute); and
  • identifying novel halotolerant bacteria that can help extract metals from ores (by Liz Watkin from Curtin University).

On top of all of that, it was great to hear about how microbes are related to the sustainable development goals and how JAMS is doing their bit to help with these goals by only partnering with sustainable organisations.

After all the fascinating talks we strolled down to Harpoon Harry for networking, awarding of the student prizes, dinner and a wonderful choice of JAMS-original cocktails from Four Pillars Gin with Stroh sustainable straws (two of the sponsors this year).

Three students from the Paulsen and Mabbut groups at Macquarie University presented posters and Belinda Fabian won the student poster prize with Ben Ford as runner up. Our posters will feature in the corridors of our department to show off the exciting microbiology work happening at Macquarie University.

JAMS_2019_posters

Ben Ford and Belinda Fabian presenting their posters at the JAMS Symposium 2019. Photo of Ben: Geraldine Sullivan; Photo of Belinda: Varsha Naidu

Thanks to the JAMS organising committee for another excellent microbiology meeting – we’re all looking forward to the next monthly JAMS meeting. For more information visit jams.org.au

Day in the life of a PhD candidate

Posted on by

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.

 

 

IMG_3760

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!

Spending time waiting …

Posted on by

IMG_3276

The first step in DNA extraction is to lyse the cells so the DNA is released. These samples are ready to go into the water bath to kick-start this process.

I’ve been doing a lot of DNA extractions this year and with that comes a lot of time waiting for the water bath to heat my samples and the centrifuge to spin. A normal DNA extraction protocol means I’ll spend over an hour just waiting for things to happen. This time really adds up over multiple experiments. These waits can come in timeframes as short as 1 minute, so there’s not enough time to get really invested in anything.

I could spend this time checking social media, but there are some things I do to make myself more productive and feel like I’m being efficient. In a short wait (up to 5 minutes) these tasks can include:

  • Reading through the next steps in the protocol
  • Preparing the materials I’ll need next – getting out the right tubes, labeling them, aliquotting a reagent and changing the pipettes to the right setting can all save time
  • Popping out of the lab for a drink of water – spending hours in the lab can mean I’m dehydrated by the end of the day, so I use these short breaks as a reminder to have a drink
  • Sticking protocols and other printed materials in my lab book – I keep a roll of sticky tape in the lab so I don’t have to spend time updating my lab book once I’m done in the lab

  • IMG_2041

    Benchtop autoclave ready to be loaded with materials to be sterilised under high temperature and pressure.

    Checking through my chemical solutions and see if there is anything that needs to be discarded or needs a GHS compliant label

  • Starting an autoclave cycle – hopefully it’ll be done by the time I’ve finished my DNA extraction and I won’t have to stay late to unload it
  • Emptying my benchtop rubbish bin – working in a PC2 lab means overflowing rubbish bins are a hazard so I do this multiple times a day

Some steps in DNA extraction have a slightly longer wait time, but still not enough to dig deep into a paper or data analysis. During a longer wait of 15-30 minutes I:

  • Load the dishwasher – clean-up is the lab duty that always needs to be done, your lab mates will thank you for it
  • Make a plan or write a protocol for an upcoming experiment – doing this in my lab book makes it much easier when I have to write up my methods for my thesis or publication later

  • IMG_2938

    Bacteria are grown on plates that contain essential nutrients. These plates have just been poured and the molten agar is cooling and drying.

    Collect the materials needed for the next day – from the storage area in the lab or the on-campus scientific materials store

  • Prepare a chemical solution I’ll need in the next few days – this could be a single reagent or a complex media with multiple components
  • Pour agar plates – the molten agar needs to cool after pouring, so it’s good to line up this waiting time with finishing off a DNA extraction
  • Complete a chemical risk assessment for a new experiment and/or make a GHS compliant label I’ll need when I make up the chemical solution
  • Edit the photos I’ve taken of experiments – that way they’re ready to print out and stick in my lab book or put into a presentation

So as you can see there are always a lot of little tasks that need to be done for a successful project and to make the lab run smoothly. Using the snippets of time that would otherwise be wasted means I have larger blocks of time to use for more intensive work that requires lots of concentration. And it makes me feel more productive.

What do you do with your 1-minute spins? Got any good productivity hacks for me?

Finding plant-microbe conferences

Posted on by

For my PhD I’m looking at genes involved in the colonisation of biocontrol (beneficial) bacteria on plant surfaces. Along with the challenge of filtering out predatory conferences, it was really frustrating trying to find meetings that would be relevant for my research area. So I thought I’d share my search strategy and the events I found so you can save time and get a head start.

There’s so many different synonyms for conference –> meeting, symposium, congress, conference, forum, seminar, event, and so on… I wanted to broaden my search without having to do every combination of words to find relevant events, so I devised a shortcut. Keywords that identified for my area of study are: plant, soil, rhizosphere, plant-microbe, microbiology, beneficial bacteria and biocontrol. I googled each keyword along with the year I was looking for. Still a lot of searches, but waaaay less than if I had to include every synonym for conference.

This is the list of conferences I came up with (in chronological order) and a summary of the information I noted down. Based on past conference dates I’ve guessed some conference timings (I’ve noted them as predicted). Let me know if you have more information on any conferences listed here or other conferences that fit in my list. As I find more conferences or more details I’ll update the list*.

Enjoy!

*last updated 31 March 2021

************

2021

Microbiology Society Annual Conference
April 26-30, 2021 – Online

Second International Congress of Biological Control (ICBC2)
April 26-30, 2021 – Online

72nd International Symposium on Crop Protection (ISCP)
May 18, 2021 – Online

11th symposium of the International Society of Root Research
May 24-28, 2021 – Online

World Microbe Forum – combines ASM Microbe 2021 and FEMS2021
June 20-24, 2021 – Online

XIX Congress of International Society of Molecular Plant-Microbe Interactions
June 25-29, 2021 – Jeju, Korea

Plant Biology Europe 2021
(bi-annual event jointly organised by EPSO and FESPB)
June 28-July 1, 2021 – Online

ASPB Plant Biology 2021 (PB21)
July 19-23, 2021 – Online

IOBC-WPRS Working Groups “Integrated Control in Protected Crops, Temperate and Mediterranean Climate”
Date TBA (tentative late August-early September 2021) – Brest, France
(Postponed from 2020 due to COVID-19)

Plant Health, Agriculture & Bioscience conference (PHAB 2021)
September 22-24, 2021 – The Hague, Netherlands
(Postponed from 2020 due to COVID-19)

PAG Asia 2021
Affiliated with the Plant and Animal Genome Conference (PAG) held in January
September 22-24, 2021 – Shenzhen, China
(Postponed from June 2021 due to COVID-19)

Harnessing the Plant Microbiome
October 22-24, 2021 – University of California, Davis, USA
(Postponed from 2020 due to COVID-19)

13th Arab Conference of Plant Protection
October 31- November 5, 2021 – Hammamat, Tunisia
(Postponed from 2020 due to COVID-19)

23rd Biennial Australasian Plant Pathology Society Conference
November 23-26, 2021 – Online

25th International Conference on Virus and other Graft Transmissible Diseases of Fruit Crops
Date TBA – Amersfoort, The Netherlands
(Postponed from 2020 due to COVID-19)

Predicted: AusME – Australian Microbial Ecology conference
(held every 2 years – last one 2019)

Predicted: 12th International Plant Growth-Promoting Rhizobacteria Workshop
(Held every 3 years – last one 2018)

Predicted: MiCROPe2021
(Held every 2 years – last one 2019)

Predicted: 7th Asian PGPR Conference
(Held every 2 years – last one 2019)

************

2022

Plant and Animal Genome XXIX
Jan 8-12, 2022 – San Diego, California, USA
(original dates: January 9-13, 2021, rescheduled to 2022 due to COVID-19)

Microbiology Society Annual Conference
Predicted: April, 2022 – UK

International Plant Health Conference
May, 2022 – location TBA
‘Protecting Plant Health in a Changing World’ – one of the key events of the International Year of Plant Health
(Postponed from 2020 due to COVID-19)

ASM Microbe 2022
June 9-13, 2022 – Washington D.C., USA

12th International IOBC-WPRS Workshop on Pome Fruit Diseases
IOBC-WPRS Working Groups “Integrated Plant Protection in Fruit Crops”, Sub Group “Pome Fruit Diseases”
June 13-16, 2022 – Plovdiv, Bulgaria
(Postponed from 2020 due to COVID-19)

4th International Erwinia Workshop (IEW)
July 2-3, 2022 – Assisi, Italy

14th International Conference on Plant Pathogenic Bacteria (ICPPB)
July 3-8, 2022 – Assisi, Italy
(Postponed from 2020 due to COVID-19)

ASPB Plant Biology 2022
July 9-13, 2022 – Portland, Oregon, USA

8th Conference on Beneficial Microbes
July 10-14, 2022 – Madison, Wisconsin, USA
(Rescheduled from 2020 due to COVID-19)

11th Australasian Soilborne Disease Symposium
mid-late 2022 – Cairns, Queensland, Australia
(Rescheduled from 2020 due to COVID-19)

Combio 2022
September 27-30, 2022 – Melbourne, Australia
Incorporates annual meetings of five Australian and New Zealand biological societies
(Postponed from 2020 due to COVID-19)

13th International Congress on Plant Molecular Biology (IPMB2022)
October 22-27, 2022 – Cairns, Queensland, Australia
Triennial conference (last one held in 2018) – (Postponed from 2021 due to COVID-19)

Predicted: 5th International Symposium on Biological Control of Bacterial Plant Diseases
(Held every 3 years – last one 2019)

************

2023

ASM Microbe 2023
June 15-19, 2023 – Houston, Texas

XX IBC 2023
July 1-7, 2023 – Rio de Janeiro, Brazil

ASPB Plant Biology 2023
Dates and location TBA

ICPP2023: 12th International Plant Protection Congress
“ONE HEALTH for all plants, crops and trees”
(Held every 5 years)
August 20-25, 2023 – Lyon, France

Predicted: Rhizosphere6
(Held every 4 years? last one 2019, one before 2015)

************
************

Past conferences: 2018

2nd Plant Microbiome Symposium
February 19-21, 2018 – Amsterdam, The Netherlands

Microbiology Society Annual Conference 2018
April 10-13 – Birmingham, UK

XV Meeting of the IOBC-WPRS Working Group “Biological and integrated control of plant pathogens” – Biocontrol products: from lab testing to product development
International Organisation for Biological and Integrated Control (IOBC)
April 23-26, 2018 Lleida, Catalonia, Spain

1st International Congress of Biological Control
May 14-16, 2018 – Beijing, China

ASM Microbe 2018
June 7-11, 2018 – Atlanta, Georgia, USA

11th International Plant Growth-Promoting Rhizobacteria Workshop
(Held every 3 years)
June 17-21, 2018 – Victoria, British Columbia, Canada

Plant Biology Europe 2018
June 18-21, 2018 – Copenhagen, Denmark

Plant Biotic Stresses & Resistance Mechanisms III
July 2-3, 2018 – Vienna, Austria

SEB Masters of Biology
July 3-6, 2018

7th Conference on Beneficial Microbes
July 8-11, 2018 – Madison Wisconsin

ISRR-10 Exposing the Hidden Half: Root Research at the Forefront of Science
July 8-12, 2018 – Israel

ASPB Plant Biology 2018
July 14-18 – Montreal, Canada

11th International Congress of Plant Pathology (ICPP): Plant Health in a Global Economy
(Held every 5 years)
July 29-August 3, 2018 – Boston, USA

ICOBM-2018 International Conference on Beneficial Microbes: Microbes for the Benefit of Mankind
August 1-3, 2018 – Kuching, Malaysia

10th Australasian Soilborne Diseases Symposium
September 4-7, 2018 – Adelaide, Australia

ComBio 2018
September 23-26, 2018 – Sydney, Australia

1st International Conference on Biological Control: Approaches and Applications
September 27-29, 2018 – Bengaluru, India

Microbes Underpinning Agriculture: Focused Meeting 2018
October 1-2, 2018 – Cork, Ireland

AusBiotech 2018
October 31-November 2, 2018 – Brisbane, Australia

International Symposium of the Plant Microbiome: Exploration of Plant-Microbe Interactions for Improving Agricultural Productivity
November 18-22, 2018 – Hurghada Egypt

************

Past conferences: 2019

Plant and Animal Genome XXVII
January 12-16, 2019 – San Diego, California, USA

8th International Conference on Polar and Alpine Microbiology
February 4-8, 2019 – Hamilton, New Zealand

AusME – Australian Microbial Ecology conference
February 11-13, 2019 – University of Western Australia

19th International Meeting on Visualising Biological Data
13-15 March, 2019 – EMBL Heidelberg, Germany

Microbiology Society Annual Conference 2019
April 8-11, 2019 – Belfast Waterfront, UK

ASM Microbe 2019
June 20-24, 2019 – San Francisco, California, USA

Biopesticide Summit 2019
July 2-3, 2019 – Swansea University, Swansea, UK

Rhizosphere5
July 7-11, 2019 – Saskatoon, Saskatchewan, Canada

8th Congress of European Microbiologists (FEMS)
July 7-11, 2019 – Glasgow, Scotland

4th International Symposium on Biological Control of Bacterial Plant Diseases
July 9-11, 2019 – Viterbo, Italy

New Approaches and Concepts in Microbiology (Symposium)
9-12 July, 2019 – EMBL Heidelberg, Germany

Canadian Soil Science annual meeting
July 9-13, 2019 – Saskatoon, Saskatchewan, Canada

Applied and Environmental Microbiology
Gordon Research Conference & Seminar
July 13-19, 2019 – Mount Holyoke College, South Hadley, MA, USA

XVIII International Society for Molecular Plant-Microbe Interactions (ISMPMI)
July 14-18, 2019 – Glasgow, Scotland

17th International Conference on Pseudomonas
July 22-26, 2019 – Malaysia

2019 International Congress on Invertebrate Pathology and Microbial Control
(52nd Annual Meeting of the Society for Invertebrate Pathology)
(17th Meeting of the IOBC-WPRS Working Group “Microbial and Nematode Control of Invertebrate Pests”)
July 28-August 1, 2019 – Valencia, Spain

ASPB Plant Biology 2019
August 3-7, 2019 – San Jose, California, USA

Plant Health 2019
American Phytopathological Society annual meeting
August 3-7, 2019 Cleveland, Ohio, USA

6th International Conference on Bacterial Blight and Bacterial Leaf Streak of Rice
August 18-22, 2019 – Cantho City, Vietnam

Arms Race: The Evolution of Plant Pathogens and Their Hosts
September 2-3, 2019 – Bristol, UK

3rd Wild Plant Pathosystems Conference
September 16-19, 2019 – close to Frankfurt, Germany

Biocontrol Asia
September 25-27, 2019 – Chengdu, Sichuan Province, China

9th meeting of the IOBC-WPRS Working Group “Integrated Protection in Oak Forests”
October 7-11, 2019 – Oeiras, Portugal

2nd Biopesticides North America Conference
October 9-10, 2019 – Orlando, Florida, USA

Meeting of the IOBC-WPRS Working Group “Integrated Protection of Field Vegetables”
October 13-16, 2019 – Stratford-upon-Avon, UK

ABIM 2019, Annual Biocontrol Industry Meeting (ABIM)
October 21-23, 2019 – Basel, Switzerland

Meeting of the IOBC-WPRS Working Group “Integrated Protection in Viticulture”
November 5-8, 2019 – Vila Real, Portugal

XIX International Plant Protection Congress (IPPC2019)
November 10-14, 2019 – Hyderabad, India

Plant BioProTech 2019: 2nd International Symposium on Plant Bioprotection Sciences and Technologies
November 19-22, 2019 – Marrakesh, Morocco

Advances in Biocontrol and IPM 2019: Addressing the Innovation Crisis
November 20-21, 2019 – Lincolnshire, UK

22nd Biennial Australasian Plant Pathology Society conference
November 25-28, 2019 – Melbourne, Australia

4th Australian Pathogen Bioinformatic Symposium (APBS)
Additional ‘workshop’ for Australasian Plant Pathology Society conference
November 25, 2019 – Melbourne Australia

Australian Society of Plant Scientists (ASPS) conference
November 24-29, 2019 – Melbourne, Australia

Ecological Society of Australia conference
November 24-29, 2019 – Hobart, Australia

New Zealand Microbiological Society (NZMS) annual conference
November 25-28, 2019 – Palmerston North, New Zealand

VIII Congress on Plant Protection: “Integrated Plant Protection for Sustainable Crop Production and Forestry
November 25-29, 2019 – Zlatibor, Serbia

MiCROPe2019 International Symposium: Microbe-Assisted Crop Production – Opportunities, Challenges and Needs
December 2-5, 2019 – Vienna, Austria

************

Past/cancelled conferences: 2020

Plant and Animal Genome XXVIII
January 11-15, 2020 – San Diego, California, USA

Microbiology Society Annual Conference
March 31-April 3, 2020 – Edinburgh, Scotland, UK
(Cancelled due to COVID-19)

14th International Conference on Plant Pathogenic Bacteria (ICPPB)
June 7-12, 2020 – Assisi, Umbria, Italy
(Postponed to 2021 due to COVID-19)

12th International IOBC-WPRS Workshop on Pome Fruit Diseases
IOBC-WPRS Working Groups “Integrated Plant Protection in Fruit Crops”, Sub Group “Pome Fruit Diseases”
June 15-18, 2020 – Plovdiv, Bulgaria
(Postponed to 2021 due to COVID-19)

PAG Asia 2020
June 17-19, 2020 – Shenzhen China
(Cancelled due to COVID-19)

ASM Microbe 2020
June 18-22, 2020 – Chicago, Illinois, USA
(Cancelled due to COVID-19, next meeting June 2021)

25th International Conference on Virus and other Graft Transmissible Diseases of Fruit Crops
June 22-26, 2020 – Amersfoort, The Netherlands
(Postponed to 2021 due to COVID-19)

Plant Biology Europe 2020
(bi-annual event jointly organised by EPSO and FESPB)
June 29-July 2, 2020 – Turin, Italy
(Postponed to 2021 due to COVID-19)

8th Conference on Beneficial Microbes
July 12-16, 2020 – Madison, Wisconsin, USA
(Cancelled due to COVID-19)

IOBC-WPRS Working Groups “Integrated Control in Protected Crops, Temperate and Mediterranean Climate”
August 31–September 3, 2020 – Brest, France
(Postponed to 2021 due to COVID-19)

16th Meeting of the IOBC-WPRS Working Groups “Biological and Integrated Control of Plant Pathogens”
September 14-17, 2020 – Gdansk, Poland
(Postponed to June 2021 due to COVID-19)

5th Korea-Japan Joint Symposium on Plant Pathology
September 14, 2020 – Tsukuba Science City, Ibaraki, Japan
Adjunct symposium with ACPP 2020 – joint meeting of The Phytopathological Society of Japan (PSJ) and The Korean Society of Plant Pathology (KSPP)
(Cancelled due to COVID-19)

Asian Conference on Plant Pathology 2020 (ACPP 2020) 
September 15-18, 2020 – Tsukuba Science City, Ibaraki, Japan
(Cancelled due to COVID-19)

Combio 2020
September 29 – October 2, 2020 – Melbourne, Australia
Incorporates annual meetings of five Australian and New Zealand biological societies
(Postponed to 2022 due to COVID-19)

ASPB Plant Biology 2020
July 25-29, 2020 – Washington DC, USA
(Meeting held online)

Plant Health, Agriculture & Bioscience conference (PHAB 2020)
September 9-11, 2020 – The Hague, Netherlands
(Postponed to 2021 due to COVID-19)

International Plant Health Conference
October 5-8, 2020 – Helsinki, Finland
‘Protecting Plant Health in a Changing World’ – one of the key events of the International Year of Plant Health
(Postponed to 2021 due to COVID-19)

Harnessing the Plant Microbiome
October 23-25, 2020 – University of California, Davis, USA
(Postponed to 2021 due to COVID-19)

13th Arab Conference of Plant Protection
November 1-6, 2020 – Hammamat, Tunisia
(Postponed to 2021 due to COVID-19)

16th Congress of the Mediterranean Phytopathological Union
November 17-20, 2020 – Limassol, Cyprus
(Rescheduled to 2021 due to COVID-19)

11th Australasian Soilborne Disease Symposium
November 24-27, 2020 – Cairns, Queensland, Australia
(Rescheduled to 2022 due to COVID-19)

************