Conference | DEZERAECOX

Terrific TDP-43 Talks in Trieste

Wed, 11 Oct 2023 12:58:17 +0000

Terrific TDP-43 Talks in Trieste

As you may know, I am currently a Lady Edith Wolfson Junior Non-Clinical Research Fellow at the University of Cambridge. My work, supported by the MND Association, seeks to develop new tools that enable us to evaluate models of MND we use in the laboratory for research and therapeutic testing. I have been focused on a protein, one of the fundamental building blocks of every cell in our body, which goes rogue in up to 97% of people living with MND. This protein is called TDP-43. It forms clumps (”aggregates”) in specialised brain cells called motor neurons, and is thought to be intimately linked to the death of these cells which underlies all forms of MND.

Recently, I had the privilege of attending the held at the beautiful Stazione Marittima in Trieste, Italy. As the name implies, this meeting was the first of its kind specifically seeking to bring together people from all around the world whose work is focused on TDP-43; from how it is encoded in our DNA, to how the protein is produced, regulated and functions in healthy cells, to how failures of its function can lead to disease. In contrast to traditional meetings focused on a specific disease or cellular phenomenon, there was a uniquely singular focus on TDP-43 and all aspects of its biology.

The meeting was opened by local host Emanuele Buratti. Dr Buratti treated the audience, spanning students to established giants of the field, to a trip down memory lane. Sharing photos of original results and hand-drawn annotations from his lab books from the late 1990’s, Buratti gave early context to a field that has gone on to span more than two decades. It set the scene for a fantastic program featuring presenters from around the globe who would go on to describe novel experimental approaches, advances in our understanding of how TDP-43 relates to MND, and new therapeutic strategies that are gaining traction toward clinical trials. Recounting it all would take longer than the meeting itself (unfortunately a case of ‘you had to be there’!) but I am delighted to have the opportunity to share a snapshot of some of the outstanding science with you.

An early highlight came in the form of a potential new therapeutic strategy, described by James Shorter in his presentation “ (Dis)solving the problem of aberrant protein states“. Recent work from Shorter’s team has focused on the normal function of TDP-43 in cells which involves the separation into a distinct phase, similar to how oil comes together to form droplets in water. If TDP-43 stays in this separated state for too long then it can turn into elongated aggregates similar to those associated with MND. Shorter’s team have , another fundamental cellular building block, to manipulate the phase formed by TDP-43 and reverse the abnormal phases. In theory, this could prevent or even reverse the characteristic clumps formed by TDP-43 in those living with MND - an exciting proof of principle that offers a promising potential new strategy toward viable therapeutics.

Competing for best pop-culture reference, Michael Ward introduced us to the TDP-43 Multiverse during his talk titled “ Functional genomic strategies to identify regulators of neuronal TDP-43 biology”. Just as big data has taken the world by storm, biology is now generating and exploiting bigger datasets than ever before. Ward’s research encourages us to ‘think bigger’ when it comes to TDP-43. Using computational tools, including different cell types and a range of biological molecules such as DNA, RNA and proteins, in an attempt to unravel the chaos that erupts in neurons when TDP-43 function is lost. The resulting data atlas may let us pinpoint the effects of losing TDP-43 function that are specific to motor neurons, a key mechanism of MND that remains unknown.

Late on the second day, Alyssa Coyne presented “ Large scale analysis of sALS and C9orf72 ALS/FTD iPSNs reveals defects in TDP-43 function repaired by genetic therapies”. In essence, a tour de force analysis of the collection of cell models created from people living with MND, which are an invaluable experimental tool. Alyssa asked a simple question, which is similarly at the heart of my research: How good are these models at capturing what we see in real people? One of the principal functions of TDP-43 is in processing RNA. RNA plays a vital role in our cells by converting the instructions from DNA to make proteins. TDP-43 processes a collection of different RNAs, which form a characteristic signature. Looking at the signature in cell models and comparing them to those of the corresponding donor allowed Coyne’s team to establish that signatures are variable between patients, just like fingerprints, but that cells can faithfully recreate the signature of their matched donor. These signatures together pointed toward defects in how molecules move within cells in MND. When TDP-43 is dysfunctional, it is found to move from the DNA storehouse - the nucleus - into the larger cell body, where it forms clumps. , again offering hope of a new potential target for therapeutic intervention.

Last but not least, the poster session — where many early career researchers showcase their work — is always a firm favourite, and this one did not disappoint. With the backdrop of a stunning sunset, attendees were treated to some stellar discussions from the future of the field. Carlo Scialò shared his progress towards the ultrasensitive detection of TDP-43 in nasal swabs; Oscar Wilkins described a new computational tool, SpliceNouveau, to help design next-generation therapies; and Diana Arseni described her groundbreaking work delivering an atomic-scale picture of the shape TDP-43 adopts when it forms the toxic aggregates found in MND. Such sessions are an invaluable opportunity to make connections, discover new technologies, and see ‘fresh-from-the-bench’ science.

In all, this really was a fantastic event spanning all manner of biochemical, biophysical, and clinical approaches to understanding TDP-43, a molecule at the heart of MND. I learnt more than I thought possible and am so grateful for the opportunity to immerse myself in this welcoming and exciting research community. I have no doubt that the collaborations forged throughout the meeting will drive TDP-43 research forward, and I can’t wait for the 2nd conference on TDP-43 function and dysfunction in disease in a few years’ time!

Can’t get enough TDP-43? Find out more about my research , or check out the complete conference program . For anyone interested in the next iteration of the meeting, stay tuned - I look forward to seeing you there!

This post was developed with editorial contributions from Charlotte Roy from the , who supported my attendance at this meeting. A version of the post first appeared .

Lorne Proteins 2020

Sat, 08 Feb 2020 05:19:01 +0000

Lorne Proteins 2020

If you’ve landed here after checking out my poster , welcome. If you stumbled here by accident, the more the merrier. Either way, thanks for stopping by!

I hope you found something interesting or useful, and enjoyed hearing about the work we are doing to develop new tools for measuring proteostasis. If you have any questions, want to know more about what we do, or simply want to get in touch, you can find me on twitter head over to the .

For anyone who wasn’t at the conference, or didn’t get a chance to say hi, I have included a brief run-down (and tried to skip over most of the gory – boring, technical – details!).

What’s all this proteostasis business?

Cells have an extensive quality control network responsible for maintaining their molecular machines, including synthesis, folding, degradation and transport

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. Collectively, this machinery is known as the proteostasis network. Proteostasis imbalance results in protein misfolding and aggregation, the central molecular signature of neurodegenerative diseases such as Alzheimer’s and Parkinson’s.

We lack knowledge of which proteins in the cell become vulnerable to improper folding during proteostasis imbalance. One measure of protein foldedness is the extent to which a protein can be unfolded thermally or with a chemical denaturant such as urea. Until recently, it has been difficult to track foldedness in cells due to sheer complexity of the many ten’s of thousands of proteins and proteoforms needed for our cells to function.

To overcome this, this work specifically aimed to:

Devise a chemical biology and proteomics approach to monitor the foldedness of the proteome.
Determine the influence of pharmacological agents that unbalance proteostasis on proteome foldedness.

What is tetraphenylethene maleimide, other than a tongue twister?!

Tetraphenylethene maleimide (TPE-MI) is a dye (tetraphenylethene maleimide) that becomes fluorescent when it binds to reactive thiol residues

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. Buried, reactive thiols are the most buried residue of all amino acids in globular (properly folded) proteins. Monitoring the exposure of these thiols using TPE-MI gives us a sensitive way to probe foldedness in complex mixtures.

To test this strategy, we used a purified, well-studied protein – β-lactoglobulin. We know both the sequence and 3D structure of this protein, and its behaviour in a range of denaturants is known. β-lactoglobulin has 5 thiol residues, of which two pairs are bonded and the remaining one (Cys121) is buried in the core of the folded protein. As β-lactoglobulin unfolds in increasing concentrations of denaturant, we get a corresponding increase in TPE-MI fluorescence.

But what about the giant protein soup our cells make, I hear you ask…

While TPE-MI can reliably tell us about the unfolding of a single, purified protein, our cells are jam-packed with thousands of copies of thousands of different proteins. How can we possibly know which proteins TPE-MI is binding to?

Enter: proteomics. This revolutionary tool is a workflow based on mass spectrometry which can report back on the composition of complex mixtures – both which proteins are present, and the relative amount of that protein. The basics of this technique are beyond the scope of this post, but if you are looking for more details check out the resources section below

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. I have included a brief explanation of the method we use below, which relies on isotopically labelling cells in culture before lysing, denaturing and labelling with TPE-MI. Proteins are digested (chopped up) into regular, smaller pieces before analysis via mass spectrometry.

Using custom software, we can identify and quantify protein pieces. Unfortunately, we cannot identify the protein pieces specifically labelled with TPE-MI, but instead, we look for the loss of those pieces. We can do this for many many proteins and start to understand the concentration at which specific proteins unfold. We can even start to understand intricacies in unfolding for separate protein domains.

How does this help us understand disease mechanisms?

This new method now provides a way to monitor how the stability of proteins (measured how much denaturant it takes to unfold them) changes under conditions of proteostasis impairment that are present in disease. For example, we are now investigating the changes in proteome foldedness when we inhibit hubs of the proteostasis network such as molecular chaperones. How do the proteins that rely on specific molecular chaperones to be folded change when those proteins are no longer active? What if we stop the cell from degrading old proteins? Or from decorating their proteins with extra modifications that mediate structure and activity like phosphorylation? Defects in this machinery are common in neurodegenerative protein aggregation diseases and we now have the tools to start tackling these questions.

References and handy links

Chiti F, Dobson CM (2017) . Annu Rev Biochem 86: 27–68.
Chen MZ, Moily NS, Bridgford JL, Wood RJ, Radwan M, Smith TA, Song Z, Tang BZ, Tilley L, Xu X, Reid GE, Pouladi MA, Hong Y, Hatters DM (2017) . Nat Commun 8: 1–10.
Lottspeich, F. (2009). . In Proteomics (pp. 3-10). Humana Press.
Graves, P. R., & Haystead, T. A. (2002). . Microbiology and molecular biology reviews, 66(1), 39-63.

That’s all from me for now. Still can’t get enough or want to know more? Simply want to get in touch? Find me on twitter head over to the - love to hear from you! Now, back to the beach 🏄🌴☀️ !

A year in review: 2019 edition

Fri, 31 Jan 2020 12:46:00 +0000

The holiday season is a time of reflection for many, me included. However, this was heightened this year, and somewhat hijacked, by the looming start of a new decade.

While there are plenty of discussions of why 2019 isn’t the end of the decade (like , and ), it did little to stem the tide of ten-year progress reports flooding . These outpourings of academic (and personal) success are often incredible and inspirational, but can also be overwhelming and disheartening for those of us who feel less accomplished.

So as is tradition, I decided to stick with my by-the-numbers account of the past year. You’ll find some wins, a handful of losses, and a few goals that looked a little different from start to finish. Finally, I look to the future and set my sights on kicking brand new goals in 2020.

Wins

A snapshot of the high points

I contributed to 4 manuscripts, of which 3 were posted as preprints
I completed my first independently-funded research project using funds totalling $40 000
I was awarded ~ $10 000 in travel awards
I attended 4 national and 2 international conferences
I presented 5 research talks, 2 posters and chaired an academic career development panel
I gave my first invited research seminar at my alma matta
I was awarded an international post-doctoral fellowship (!)
I performed over 45 (mostly week-long) experiments in just 159 working days, and over 75% of these gave useable results
I wrote or edited over 30 000 lines of code
I was an active member of 4 conference and professional committees, and an ordinary member of 4 professional societies
I directly supervised 3 students and informally mentored at least 4 others
I attended a 5-day leadership course, making 5 new connections that have blossomed into 3 new collaborative relationships
I accounted for each of my working days by posting a reflection to a purpose-built Instagram profile, receiving a total of 3191 likes
I authored 10 blog posts containing a total of 14 642 words, which received 5437 views from 3849 visitors across 36 different countries - more than half of these views were on a single post after I shared it with the Twitterverse!
I slept an average of 7 hours a night, did an average 6260 steps per day, and lost 12 kilograms
I read 1 1/2 more books than last year and completed 1/4 of my first ever attempt at cross stitch
I gave my very first tech talk at a local meetup group
I travelled to 3 countries and explored 5 new cities, and took 2571 photos
I spent 365 days being a partner, sister, colleague and friend - being a happy, (mostly!) healthy human

Losses

A snappier shot of the low points

Only one manuscript made it through the review process to be published
None of my first-author manuscripts are any closer to being submitted
Of the 431 papers I downloaded, I read less than 10% of them in full
I am not proud of my ‘bedside manner’, as I was impatient and frequently frustrated with students
I spent over 50 hours preparing 5 unsuccessful grant or fellowship applications
My coding projects are still in a state of disarray, in desperate need of a tidy and some documentation
I only read 3 1/2 books and put 12 kilograms back on
There were days where I barely slept 4 hours and struggled to make 1000 steps
I only took 11 days of leave, and was fuelled by stress and anxiety far more often than passion and curiosity

Lessons

The bits I wish I knew at the start of 2019, but had to learn the hard way.

You have to crawl before you can walk - academic conferences are great, especially the chance to travel internationally. However, you have to have the time and effort already committed to a project to have something new and interesting to present, and in turn to make the most out of the experience.
Time tracking - the more you know! There are already people using your personal data to sell you shoes and expensive holidays - why not use your personal data for good, not evil? Late in 2019, I started tracking how I spend my workday (keep an eye out for more details coming soon!), helping me refocus on my goals, dedicate productive time to important work and better plan my time for specific activities according to how long it had taken in the past.
The sunk-cost fallacy - Sometimes you have to cut your losses and move on, despite having invested so much time and effort and energy into one particular thing. If it’s not right, or not happening, maybe it never will be. And that’s ok - sometimes you have to empty some space to leave room for the next great thing, whether that’s the next big experiment or project, or the next townhouse or friendship. However…
Perseverance is key - every application makes your next application better. Although, being privileged enough to be able to persevere is a huge source of diversity challenge in academia. Appreciate when you have the option to continue chasing a dream, and not just when that dream becomes reality.
Decisions are hard - and making them can change the course of your life immediately, even in how you feel about the people around you.
Some people will never understand - and that’s on them, not you. Living your best life is unlikely to please everyone, so live a life you’re proud of and whether others understand your path or not is irrelevant.

Goals

This time last year I set some goals. This was a new approach to goal-setting for me, and I’m pleased that it worked (moderately) well! Physical activity was a consistent focus - even if only a short walk in the afternoon, I was conscious of the link between how my brain and body feel. I made substantial progress on building reflective practices and, last but not least, I landed the next job!

Building on this foundation, here are my goals for 2020

1. Papers are paramount. With a looming international move, I have a little over six months to tie-up all my projects and get my first-author manuscripts over the line. My goal is to finalise three publication-ready first-author manuscripts by April. With drafts floating around in various states of disarray, I will use structured writing time for at least eight hours a week to make focused progress. I will use calendar entries for accountability and maintain a master task list for tracking progress. I would also like to reorganise my reading and writing process and systems, but that’s a goal for another time!

2. Hacking hand-over. Part of the leadership course I attended encouraged us to think about ourselves as changemakers. This could result from our science, or more broadly our leadership, but nonetheless we were to imagine what change we wanted to make in the world over the next year. Then we had to plan it. Who would we connect with? What skills/tools did we need? I have always been a passionate advocate for programming for life scientists, and I would love to be the catalyst for this in our institute - to take the plan I sketched on paper (yes - real-life butchers paper!) and put it into action. My goal is to establish a local hacky hour at my institute, bringing together experienced, amateur and coding-curious researchers in a collaborative space to learn from each other. I will gather a small working group of researchers experienced in programming by the end of February, where we will brainstorm the best structure, location and time for meetups. The action items from that meeting will serve as a task list for tracking progress, and I will coordinate at least three hacky hours before handing over the reins when I move.

3. Blog better. Despite averaging one post per month last year, I felt there was a lack of substance with so many conference wrapups and few useful, practical or probative posts. The one obvious exception was a rather popular commentary on the state of NHMRC Investigator Grants. This was a combination of an important issue and a good coding project, and I would love to produce more content like this in the future. My goal is to continue posting at least once per month, of which half will pursue practical or probative themes. This will be easily tracked by my posting record here, so feel free to help me stay accountable!

4. Healthy is happy, and mindfulness matters. As I approach another decade of life (that’s right, a big three-oh this year), I am starting to appreciate that a healthy body and mind is not really something you can achieve. There is no box to tick to say you are done, and there isn’t really a finish line. A commitment to maintaining your physical and psychological health is lifelong, and relapses will happen when you aren’t paying attention. My goal is to recover my healthy habits, focusing on yoga and reflections once a week. My progress will be easily tracked by my health app (thanks technology!), and I will continue to maintain my purpose-built Instagram account with weekly posts. For the safety of me and my lab mates, that account will stay anonymous - but it serves as a neat record for me at least!

2019 was undoubtedly one of the hardest, but most rewarding years yet. Just when I finally felt comfortable in my space and role in Melbourne, I landed an international Fellowship - a huge win that is equal parts exciting and terrifying. As they say, life begins at the edge of your comfort zone. So here’s to an adventurous, unknown 2020 - may it be filled with science, self-exploration and smiles.

Image credits: @brookelark via

BioInfoSummer 2019

Sun, 29 Dec 2019 09:28:44 +0000

With half my home state on fire and the lead up to Christmas, this post has been in the works for a few weeks. But here it is - better late than never! My brief recap of my recent adventure to BioInfoSummer 2019.

Conference details

Title:

Date: December 2nd - 6th 2019

Location: University of Sydney, Australia

Overview:

BioInfoSummer brings together advanced undergraduate and postgraduate students, researchers and professionals from the mathematics, statistics, medical sciences and information technology disciplines. Attendees develop bioinformatics skills, national networks and employability. The central themes of the 2019 conference were Epigenetics/genomics, Single cell omics, Mass spec analytics and BioCAsia/precision medicine.

Overall thoughts and impressions

Of all the conference travel I have done this year, BioInfoSummer was the closest to home and the furthest from a normal conference. The wide applicability of omics techniques meant a broad spectrum of research topics presented by a diverse collection of researchers with a common love for data analysis. In addition, being targeted at students and early-career researchers meant the dynamic of the seminar sessions was quite different - an atmosphere in which students were comfortable asking questions and driving the discussion around world-leading best practices in the field of bioinformatics. This was supported by plentiful and generous travel scholarships boosting the participation of interstate early-career researchers.

Even though my research has been edging into bioinformatics for a little while, this was my first formal foray into the community. While I was a little anxious about being immersed in a new group of people, luckily bioinformaticians are a friendly bunch! This meant that the workshops had a welcoming feel, creating a safe space to actively try out the techniques presented during the morning symposium sessions.

Last but not least, the location and timing of BioInfoSummer meant that they were able to share sessions and speakers with , and were followed directly by . This enriched the sessions and provided even greater diversity and networking opportunities. This truly was a fantastic blend representative of the bioinformatics scene in Australia. I cannot recommend enough for new PhD students or post-doctoral researchers new to bioinformatics in it’s many incarnations.

Lessions learnt

1. Bioinformatic techniques for proteomic analyses lags behind the trail blazed by genomics - this was evident in the distribution of the program, but also attendees. However, I also think that…

2. The distinction between proteomics and genomics is sometimes unhelpful - similar underlying data structures make some methods applicable to both, and leveraging the substantial ground that has been covered in genomics will assist in the rapid progression and development of proteomics methods.

3. Single cells are the future, but not the complete story - innovations in single-cell proteomics and ongoing developments in single-cell RNAseq will continue to push the boundaries of our understanding of biology on the smallest scales. However, one of my favourite talks of the conference was on the value of bulk methods in an era of single-cell capabilities. And I agree - these methods should be applied as appropriate and often one and inform the other.

4. Seeing is believing - two-dimensional imaging mass spec and spatial transcriptomics are the next frontier. With these techniques, we are starting to understand the spatial distribution and cooperation of cells in health and disease.

5. The future is now - the big data buzzword - everyone will have heard the term big data. This is becoming more the norm than the exception, even in biological research. This has meant that method development and bioinformaticians are in high demand, and become recognised as an integral part to any research project. This was exemplified by one of the conference keynotes, in which the speaker discussed the essential skills for a bioinformatician in the next five years; many of these included the ability to wrangle, access and store large amounts of data, as well as being able to leverage this data for biological insight.

6. Unexpected acquaintances - I travelled to Sydney expecting to know no-one. In a classic small-science-world moment, within five minutes of arriving I ran into a post-doc from another research group in my building! While we had met and talked a little previously, the chance to spend a week nerding out over data analysis and coding methods was the perfect way to get to know each other better. In fact, this was one of the best parts of the conference. As well as this, I met a handful of people from my alma mata who grew up in a similar corner of the world as I did.

Take home resources

There were too many great resources to share them all, but if you’re looking for tutorial style activities then the Material for each of the is a great place to start. Other than this, below are a few of the packages, tutorials or databases that I am keen to check out after hearing about them during the conference:

’s featured workspaces demonstrate common genomic analysis pipelines deployed using data and tools available on AnVIL.
is a portal to a series of public experiments describing mouse and human stem cells and how they differentiate to become mature cells, tissues and organs.
is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data.
: A Python Library for High-Throughput (Phospho)proteomics Data Analysis
The repository contains a list of open source Python tools for Proteomics analysis. The list is very likely incomplete and we are happy to take pull request with new tools.
The workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language.
workflow: differential discovery in high-throughput high-dimensional cytometry datasets

These will hopefully give you a flavour of the overall themes covered at the conference, but if you are new to the world of bioinformatics I thoroughly encourage you to get involved next year. The conference is slated to be held next December in Canberra, so keep an eye out for the official announcement!

Overall, BioInfoSummer was a great opportunity to connect and build community with like-minded people. I was so lucky to be supported by an AMSI ChooseMaths travel award - without their support, I could not have travelled to attend the conference and I cannot thank them enough for their support of Women in STEM. If you are new to or interested in the world of bioinformatics I whole-heartedly recommend checking it out next year!

Image credits:

Toolbox Talk: Scientific posters

Tue, 30 Jul 2019 10:39:57 +0000

Going to a large, often international, conference jam-packed with superstars in your field is one of the privileges of being a scientist. Conferences are essential for building your network, keeping up-to-date with the progress inside your niche and more broadly in your field, and establishing or maintaining collaborations. If you’d like to know more about my conference experiences, check out . I was lucky enough to attend and present short talks at a few conferences in 2017, and it was a wonderful opportunity to show the scientific community what I have been working on.

However, there are only so many oral presenter slots available at such events, and often these are used by the organising committee to highlight the very best and newest science. But what about the rest of us? It can be really difficult to get the most out of a conference, especially as a student, if you don’t have an opportunity to showcase your work. Enter: poster presentations.

Wait, like in elementary school?

If you are thinking of a giant piece of butcher’s paper, covered with scribbles in multi-coloured permanent markers, you aren’t too far wrong. But things have evolved a little since the school days, and we do have slightly more developed tools for displaying our work these days. Unfortunately, making an engaging scientific poster is often not something we are formally prepared for during our scientific training. We are being moulded into the next generation of scientists, after all - what no one tells you is that artist is just one of the many additional hats that you will wear often as your career progresses.

With this in mind, I thought I would share a little about my process and tools for making an engaging poster. It is by no means a one-stop-shop, as every time I make a new poster I learn a little more about the process, but hopefully, you will find something useful as you prepare for that next science-filled conference adventure.

Tools

There are plenty of purpose-built design software packages out there specifically for making commercial posters, and some even targetted at producing scientific visuals. I have included a few links in the additional resources, but to be honest, I have had mixed success with these - if you find any that I have missed or that you’ve found particularly helpful to let me know!

In the meantime, I have settled on a combination of a freely-available vector graphics program (Inkscape) for compiling individual panels into standalone figures and presentation software (e.g. or ) for the overall poster design. If you haven’t heard of vector graphics programs before, or are unsure why you might want to use one, you can read more . In essence, because of the way they are constructed, vector graphics are easy to manipulate and can be scaled indefinitely without losing their quality as they are not composed of pixels, in contrast to the raster-based file types jpeg and png.

For data-laden figure panels, I will usually stick with python or (if you are interested in this, check out some of my other toolbox posts ). For any work dealing with protein structure, is your friend. The learning curve can be quite steep (I am only just now mastering the basics of opening a structure file, editing the colours and changing the display type from ball and stick to ribbon!) but it is relatively easy to produce a striking visual that will aid in any handwavy descriptions of a protein’s structure. Keep an eye out for my beginner’s basic guide to PyMol in a future Toolbox Talk!

Last, but definitely not least, I use a to create a link to this website. Even if the name is not familiar, I am sure that you would have come across in the wild before - they are a type of matrix barcode that links to a website or application when scanned with a smartphone camera. There are plenty of free online platforms for creating your own QR codes, and many that give you the ability to adjust the shape and colour of the individual elements, however be careful to know the difference between static (meaning you have no flexibility to adjust where the link directs after printing) or dynamic (that contain an automatic redirect which you can adjust after printing) to make sure you get one that suits your particular needs. I have found this especially handy for posters - by encoding your contact details or link to your website, it is easy for conference attendees to get in touch without having to hastily scribble down your email on their crumbled napkin.

Techniques and tips

Even the most exciting and life-changing data can find itself on a poor poster. There are many unwritten (and written) rules for making an engaging and eye-catching scientific poster, and many more experienced people than I have written guidelines and tips, some of which you can find in the resources section below. In any case, I thought I would throw in a few of my trusty tips here:

Layouts should be simple and easy to follow. I find that creating boxes to guide the reader through the poster in a logical fashion can be helpful. Remember a poster is about walking someone through your science and stories that jump backwards and forwards can make it hard to stay engaged. As a general rule, try not to require your audience to do too many optical gymnastics to follow the narrative of your science. When creating a new poster from scratch, I like to sketch out the layout, brief text tidbits and figure ideas by hand in A4 format to help get a handle on what data I need to track down and figures I need to produce. I also find drafting this initial layout in A4 size helps to keep my final poster from getting too overcrowded.
Find SVG versions of logos for the institutes that contributed to the work. It is good practice to acknowledge the financial support any project receives, and posters are no exception. In practice, I typically will have anywhere from 1 - 3 logos on my poster and any additional smaller contributions can be acknowledged in the text if you feel it is necessary. I will always find SVG versions of the logos, such that they can be edited and resized without losing any quality. Generally, you will be able to access these from your University brand team, or a quick google search with an advanced filter to find SVGs works well too.

Never underestimate the power of a good colour scheme. There is nothing worse than a poster that looks more like a rainbow kaleidoscope than a scientific document. Try to steer clear of elaborate colour schemes, and away from anything too light or bright. Also, keep in mind that picking a simple colour scheme to use throughout the entire poster (e.g. one type of sample is the same colour in all panels) helps to provide continuity for your reader. For those who are colour-coordinator challenged, a quick google search for colour palettes will provide all the inspiration you need.

Remember the power of size, shape and colour for drawing attention. With the limited time and large amount of information available at poster sessions, conveying the most important points from your work is crucial. Using accent colours, bold fonts or larger sizes can help to draw your reader’s eye to the key aspects of your work, and hopefully prompt them to ask more about the details!
Consistency is key. A poster, aside from displaying scientific results and information, is at the end of the day a piece of art. As with any beautiful artwork, the little things matter! Use the handy aligning and specific dimension setting functions in powerpoint to make sure everything is balanced and consistent. Check that the text sizes, fonts, line widths etc are identical throughout your poster, especially for things like headers and panel outlines. There will always be one or two typos that sneak past you, but it’s also a good idea do several final read-throughs to check for typos - once your masterpiece is printed, there is no turning back!
Print smaller versions for proofing. Printing an A4 version of your poster is a great way to check for readability and those last-minute alignment or spelling errors. As a general rule, anything that is not readable in this format will not become more-so simply by being printed bigger - remember you want to be able to engage your visitors in conversation, not have them glueing their nose to your poster trying to make out the details!
PDF is your friend. Particularly if you include transparent artwork or special characters, it is good practice to export your poster from powerpoint to PDF before submitting for printing. There are also a few tricks with powerpoint to ensure the quality is maximal, which can be found in the ‘Options’ menu of the dialogue box during export.
Be prepared to print early. Some institutions have their own print services, and these can be a cost-effective way to have your poster printed. I have a lot of experience with Officeworks and have generally been thrilled with their service, although I would recommend visiting a store in person to submit and collect your poster. They will generally give you a test print which is handy to make sure your creation survived the file format change. Regardless of which route you choose, plan to have your poster finalised and printed several days before departure - this way you will have a few days up your sleeve to handle the inevitable curve-balls!

Useful resources

from Animate Your Science has some straightforward tips for layout and content. I will admit to disobeying a few of their “rules” but generally great advice!
Toolbox talk on and the

Did I miss your favourite tool or technique? Find me on or head over to the to tell me more!

Image credits: codytdavis, greyritualstudio, alecuffia and arterbury via

FASEB Protein Aggregation Conference 2019

Sun, 30 Jun 2019 04:29:41 +0000

After a science career spanning a decade without having attended an international conference, I have been fortunate enough this year to speak at not one but two! What follows is a not-so-brief rundown of my second international conference, what I learnt along the way and where I am hoping to take these lessons.

The benefits of a niche, narrow-focused conference

From the very first keynote speaker (shout out to Judith Frydman - what a powerhouse for proteostasis research), it was clear to me that this was going to be different to almost any other conference I have attended in the past. This conference (and in fact, the same is true for most FASEB themes) was very targeted around a single area of biology (protein aggregation), meaning that the talks were all very focused and relevant for all attendees. Indeed, the tight-knit and collaborative nature of this community was exemplified by the fact that each speakers acknowledgement slides listed at least one - normally many - other attendees.

It was so refreshing and heartening to see a dedicated community of brilliant researchers converge around this problem with a singular view to solving the puzzle of disease-associated aggregation. As well as this, there was a broad range of techniques on display and I felt that I left with a fantastic cross-section of the breadth of work being done in the field, both for pathogenic and functional amyloid aggregation, ranging from single-molecule through structural, cellular and whole-organism studies right up to clinical trials. Importantly, plenty of researchers presented unpublished data (presumably due to the diminished need for an extensive background in this audience, who are likely to have seen the speakers published works) that I would otherwise not have seen for many more months/years if the paper is held up during publication.

For me personally, this conference represented the intersection of my PhD work (centred on aggregation of a specific protein) and my current postdoctoral work (focusing more broadly on proteostasis and its role in disease-associated protein aggregation). So much has happened in the field since my PhD and it was pure bliss getting to nerd-out surrounded by like-minded people. I was surprised more than once at the new connections my brain was able to find in this setting. I found that by listening to many perspectives/methods targetting similar biology, it was easier to start to integrate those complex ideas rather than reading the papers in isolation. Aside from this, for the junior attendees like myself this conference made for a fantastic job market, with many lab heads in our field advertising positions.

Lessons learnt

A good and engaging speaker is one who is in tune with the audience, including their level of engagement, and who respects the time of the audience by sticking to their allocated slot.
Aim to engage. In a small group such as this, you will inevitably run into many of the high-profile speakers - maybe even at the breakfast table! - so it is essential to have attended and engaged with their talk. Bonus points for devising an intelligent question to follow up on their presented material!
The “comment and a question” audience member will always elicit a collective groan - don’t be this person!
Conference organisation is no small feat - but inevitably the strength of the organisation team will impact on the general experience. In this case, a lack of confirmed program less than a week out from the conference was not a good sign. Missteps in the organisation led to the chaotic herding of humans to food and coffee breaks and program potluck ensued when the speaking slots were revised on day one of the conference.
Location, location, location: Snowmass was an incredible conference location. A small ski village easing into the break between winter ski and summer hiking seasons, there was plenty of sunshine and a brisk breeze all set in front of a stunning snow-capped mountainous backdrop. A huge highlight of the conference was the relative isolation which, while difficult to travel to and from, heightened the sense of community and connectivity between attendees. Spending time immersed in the location will strengthen your connection to that conference. Snowmass made this particularly easy, with plenty of Springtime hikes, walks and sunshine on display.

The who, what, when and where of woeful wifi - an outstandingly woeful conference internet connection elicited plenty of complaints throughout the week. However, I did feel was more engaged with talks that I might not have otherwise prioritised, as it was much more difficult to multitask with attention-sucking admin jobs like email. While sticking almost 100 researchers in a room for large swaths of the day that does not have reliable internet is probably a recipe for disaster, it certainly supports the age-old adage of ‘unplugging’ during seminars/conferences to be emersed in the research at hand.
Chairing is caring - an experienced chair who takes control of a session, including speaker introductions and managing question time, can have a profound impact on the speakers and attendees. It is not a job that should be taken lightly. It is worthwhile paying attention next time you have the chance to observe an adept chairperson, taking note of the often unseen acts that contribute to a flawless, inclusive and positive conference session.
The diversity debate among question askers - it struck me how often the same group of 5 - 10 people in a room of ten times that many were always the ones to ask questions. I have never taken to the microphone at a conference to ask a question of the speaker. Not due to lack of ideas - I will often have a list of question ready and waiting to be addressed - but I always lack courage in a room filled with ’experts’ and my imposter syndrome keeps my butt glued to the seat. Is this maintained as some kind of PI-ready test you have to pass? Throughout this conference, I ruminated on the idea of how to engage people other than those that are brave enough to take to the microphone - there are plenty of free crowdsourcing options out there ( and to name a few), and yet I have not seen a single conference where this is adopted. I am keeping a keen eye open for an opportunity to put this inclusivity initiative into action.
By far the biggest take home from this conference was that everything which seems so significant before leaving for the conference (poster prep, student meetings, experiments, slides, …) will no longer be so important once you arrive, and will be overcome by things like remembering faces of people you meet, feeling comfortable in a room of strangers, testing the confines of your comfort zone and nailing your two-minute “who I am” pitch. I am still working on perfecting these aspects of conference attendance!

Personal perspectives

“Growing a pair” is a lifelong process: it is important to make the most of opportunities at a conference (which can often be once-in-a-lifetime combinations of people, place and perspectives) while understanding and appreciating your limits.
Finding your people and your place: while engaging with diverse people is a key goal of attending any conference, recognising that you need smaller groups and its OK to need more relaxed time (e.g. spending time with small group of colleagues for drinks at a local bar instead of the crowded networking events.

The psychology of ideas: you know that feeling when your idea is discussed during a meeting, and the academic goes on to believe it was theirs? For the first time ever, a senior academic articulated to me their inability to discern where an idea comes from, and it was enlightening. In contrast to my previous reactions, this wisened academic encouraged me (and the other early career researchers present) to hold firm when this happens and to realise that it is most often without malice but simply a product of the multitude of ideas and meetings senior researchers attend every day.
The importance of a mentor in science: it’s no secret. In fact, any time I have spoken to an academic about their career path and trajectory they speak constantly about the different mentors that smoothed their journey. But this conference, I spent a bit of time reflecting on the importance of proactively approaching search for good mentor-mentee relationships. Having mentors that enter your career organically is important, but you should also identify and target strategic additions to your ’team’ of mentors.
Who am I? Every successful and prominent researcher to take the stage at this conference began with “My lab works on…”. It is important to define this early on, and I am very aware of this hole in my current career focus.
The value of contemplation: Conferences have been one of the few times this year that I have taken the chance to sit and think - really think - about science (and life and decisions). While I would like to bring more of this deep contemplation to my every-day science, I am learning to accept and expect these events to be heightened moments of reflection and embrace the soul-searching mood!
Trading hats: with a few days set aside before and after the conference for travel, it was incredible to put on my long-lost tourist hat and enjoy the sights, sounds, smells and sensations of being in a new country. This experience reminded me of how lucky I am to have the opportunity to do this as an academic, and that I should more often take time to reflect on that privilege.

Overall, this conference was a tour-de-force of world-leading experts and cutting-edge research, and included several abstract-selected talks from ECRs (including myself!) that together comprised a diverse and wellbalanced program in a stunning location. Were you in Snowmass this June? Get in touch via and let me know what you thought of the FASEB Protein Aggregation Conference!

Banner image credits:

EMBL Proteomics in Health and Disease Mechanisms 2019

Sun, 24 Mar 2019 07:19:06 +0000

Last year I had the privilege and pleasure to attend (and present at) four scientific conferences. This year is shaping up to be just as wonderful, as I have been lucky enough to attend two conferences is as many months, marking the start of what I hope to be a productive year ahead. Here is a little about my recent European adventures, including my first oral presentation at an international conference.

Conference details:

Title:

Date: 7th - 9th March 2019

Location: Heidelberg, Germany

Overview:

Focused on the application of proteomics to cell biology and unraveling disease mechanisms by addressing conceptually novel ways to study long-standing questions in these fields. As most proteomics-based conferences tend to focus on analytical chemistry, the selection of biological topics is usually uneven. Therefore, this unique conference aims to showcase biology applications and build bridges to the disciplines where the technology’s promise is still not nearly fully realised.

There’s a first time for everything!

This was my first truly international conference. What do I mean by that? I have attended and presented at several Australian national conferences consisting of international speakers, but was yet to have travelled overseas to visit a conference in another country. Unfortunately, our isolation makes such an undertaking on a student or starting post-doctoral salary near impossible. In this case, I had been madly applying for every pot of travel funding I could find for the last year, and in a fantastic “it-never-rains-but-it-pours” moment I received all three of the grants I applied for! This meant I was able not only to travel halfway around the world and attend a pre-eminent conference in my field, I could also afford to visit some long-term collaborators for a week afterwards. All together, the two weeks of travel were almost entirely covered and this meant that instead of being consumed with the cost of my every move I could actually focus on the science.

Overall scientific programme and conference feel

Not only did I get to hear about all the amazing developments at the forefront of proteomics research worldwide, I also got to showcase some of my work to leaders in the field. This was an incredible opportunity, and while I was a little disappointed with my talk (owing to sub-optimal preparation and a large dose of nerves), I received overall positive feedback. As well as this, there was so many advances in techniques and biological understanding that I would have never come across on my own, at least not within the next 12 months while the papers are being sucked down the peer-review black hole!

As well as a stunning program, I feel I must give a bonus shout out to the EMBL organising team. Everything ran smoothly, was well organised and timed, and was superbly catered. There was also a small enough number of participants and a well-balanced program between students, post-doctoral researchers, principle investigators and moguls of the field. A conference I would highly recommend to anyone interested in the biological applications of advanced proteomics techniques.

So conferences are just an excuse to travel?

Conferences are the life-blood of academic knowledge sharing. You might think the enormous volume of published literature would be the best source of the up-to-date goings-on of the science world, but sadly in most circumstances you’d be wrong.

I have written before about the importance of conferences, particularly for those of us a little isolated outside the major American and European science hubs. This is because these conferences are essential for establishing and maintaining connections with colleagues, and for hearing about the cutting edge research being done in your field all over the world. As I alluded to above, unfortunately by the time most manuscripts have made it through the academic publishing process, six to twelve months have past (sometimes more) and there are more new and exciting developments already happening (with the advent of preprint servers such as BioRxiv this will hopefully change, but more on that in a later post).

For these reasons, conference attendance in particular for early-career researchers, is about so much more than the travel. Sure, it helps if the places you are visiting are enticing and if you can spare a few days afterward to explore, but the invaluable aspects of conference attendance always take precedence.

Lessons learnt

As my first international meeting, I learnt some new lessons about attending (and making the most of) conferences abroad.

1. Multiply your typical organisation time by at least double. International travel, in addition to conference attendance and accommodation, requires a significant investment of time and energy to plan and book a reasonable itinerary.

2. Departure day is not that far away. I realised after madly rushing to finish my slides on the 14 h flight from Australia to my stopover, that I had perhaps underestimated how quickly my departure date would approach. I was so focused on tackling the seemingly all-so-important last minute experiments and meeting with my students to plan their activities while I was away, that the very reason for my trip got pushed to the side. The result was a less-than-flattering performance during my presentation, and a general feeling of exhaustion throughout the conference which dampened my social spirit. Consequently, I did not proactively initiate many interactions with other attendees, and therefore failed to make as many useful contacts as I otherwise could have.

3. Do your research, researcher! This mostly relates to scoping out the program beforehand. Sure, reading the headline speakers you should be able to identify any leaders that would be good to hear from. But more than this - look over the abstracts, and pinpoint those which are relevant, interesting or potentially useful. To assist this process, concurrently search the presenter in PubMed to get a handle on their other research. Unfortunately, an abstract may not do justice to a programme of scientific discovery, however reading the most recent/most cited articles will help you highlight not-to-miss talks. In addition, I got caught out this conference by an invited speaker whose most recent papers have been instrumental in my project design. Unfortunately, I recognised the first author’s name, and not the speaker (who was senior author on the papers in question) and therefore missed an initial opportunity to discuss this work in depth with the driving principle investigator. Having then done my homework, I was able to make this crucial connection.

4. There will be other conferences, but this is a once-in-a-lifetime experience. Sure, there will be uncomfortable moments, especially attending a conference in a foreign country surrounded by unfamiliar languages and faces. But the best in life happens outside your comfort zone. Unfortunately, it took me a significant portion of the short three-day meeting to push my comfortable boundaries, and after the first two days I left feeling as though I had not taken enough advantage of the opportunities a small meeting with superstars-of-the-field presents. I was disappointed in the impression I made over these two days due to my lack of will power to engage in the social activities, and this was compounded by the feeling of responsibility to those who had funded my trip (including the conference organisers, with a very generous stipend). Ultimately, by the end of the conference, I gathered the seeds of a few meaningful connections to chase up by email - and the very important lesson to make more of these meetings in person in future.

Final thoughts

There are plenty of downsides to science (hellloo no job security, poor work-life balance etc) and travelling (long-haul flights, little sleep, $$$) - but conferences provide a great opportunity to combine the best of both. I would thoroughly recommend this conference, or any in the series of , for early-career researchers looking for an excuse to visit Europe and beyond.

Have you attended any other international conferences or EMBL events you can recommend? Find me on or head over to the to tell me more!

Many thanks to the generous funding provided by the Bio21 Institute Post-doctoral Fellows Travel Grant, the University of Melbourne Faculty of Dentistry, Medicine and Health Early-career Researcher Travel Award and the EMBL Corporate Partnership Programme Travel Grant. Without these initiatives, this travel would not have been possible and I am so very grateful for the opportunities provided by these funds both at the conference and beyond.

Image credits: EMBL Conference logo sourced

#LorneProteins2019 & #FASEB2019

Mon, 11 Feb 2019 06:07:09 +0000

If you’ve landed here after checking out my poster or the , welcome. Thanks for stopping by!

Just can’t get enough of the pretty pretty science? You can find details about the work I presented on my poster here. For anyone who wasn’t at these conferences, or didn’t get a chance to say hi, I have included a brief run-down (and tried to skip over most of the gory - boring, technical - details!).

Now - onto the science!

Setting the scene.

Cells have an extensive quality control network responsible for maintaining their molecular machines, including synthesis, folding, degradation and transport

\[1\]

To overcome this, this work specifically aimed to:

Devise a chemical biology and proteomics approach to monitor the foldedness of the proteome.
Determine the influence of pharmacological agents that unbalance proteostasis on proteome foldedness.

What is tetraphenylethene maelimide, other than a tongue twister?!

Tetraphenylethene maelimide (TPE-MI) is a dye (tetraphenylethene maelimide) that becomes fluorescent when it binds to reactive thiol residues

\[2\]

To test this strategy, we used a purified, well-studied protein - β-lactoglobulin. We know both the sequence and 3D structure of this protein, and its behaviour in a range of denaturants is known. β-lactoglobulin has 5 thiol residues, of which two pairs are bonded and the remaining one (Cys121) is buried in the core of the folded protein. As β-lactoglobulin unfolds in increasing concentrations of denaturant, we get a corresponding increase in TPE-MI fluorescence.

But what about the giant protein soup our cells make, I hear you ask…

Enter: . This revolutionary tool is a workflow based on mass spectrometry which can report back on the composition of complex mixtures - both which proteins are present, and the relative amount of that protein. The basics of this technique are beyond the scope of this post, but if you are looking for more details check out the resources section below

\[3-5\]

Using custom software, we can identify and quantify protein pieces. Unfortunately, we cannot identify the protein pieces specifically labelled with TPE-MI, but instead we look for the loss of those pieces. We can do this for many many proteins and start to understand the concentration at which specific proteins unfold. We can even start to understand intricacies in unfolding for seperate protein domains, such as in the example below where different reactive thiols give information on specific domains of Hsp70.

How does this help us understand disease mechanisms?

References and handy links

Chiti F, Dobson CM (2017) Annu Rev Biochem 86: 27–68.
Chen MZ, Moily NS, Bridgford JL, Wood RJ, Radwan M, Smith TA, Song Z, Tang BZ, Tilley L, Xu X, Reid GE, Pouladi MA, Hong Y, Hatters DM (2017) Nat Commun 8: 1–10.
Lottspeich, F. (2009). In Proteomics (pp. 3-10). Humana Press.
Graves, P. R., & Haystead, T. A. (2002). Microbiology and molecular biology reviews, 66(1), 39-63.

That’s all from me for now. Like the pretty pictures? Still can’t get enough of the science? Simply want to get in touch? Find me on twitter or head over the to page - I’d love to hear from you! Now, back to the beach 🏄🌴☀️ or the snow-covered mountains 🏔️⛷️!

Lorne Conference Series 2018

Sun, 11 Feb 2018 05:31:58 +0000

At this point, I think I have written more about conferences than anything else. I am sure you are thinking that is all scientists do - Don’t be fooled! I have been incredibly fortunate to get to so many conferences in the last few months, culminating in two iconic fixtures in the Australian protein science conference circuit - Lorne Proteomics and Lorne Protein Structure and Function. I wont belabour the point about how important or valuable these conferences are (at this point, it gets kind of redundant!), but I will give a quick overview of my experience of the Lorne Meetings 2018.

First, it is important to understand the origins of the Lorne meetings. Starting out in the 70’s as a humble symposia, the Protein Structure and Function Meeting this year celebrated it’s 43rd installment. It is now at the centre of five consecutive meetings that run throughout February in the lovely beach town of Lorne, Victoria, covering Proteomics, Proteins, Genomes, Cancer and Immunology. I have been to a few of the Proteins meetings throughout my PhD, but this is the first time that I have attended two of the Lorne meetings back to back. It gave me a unique perspective on the similarities and differences of each meeting, and I benefited from each in wildly different ways.

A nice feature of the Lorne meetings is that the experience starts during the transit to Lorne. This year I traveled with one of my supervisors, and it was a great opportunity to have some one-on-one time. If you ever get the chance to travel with your academic mentors, I highly recommend grabbing it with both hands! It is through these conversations that you can get to know the person behind the science, and the politics behind the academic. For me, these conversations have been a highlight over the years, and this was no exception.

The first in my lineup was Lorne Proteomics. Given proteomics a very new skill to me, this was a great opportunity to get up-to-date knowledge from leaders in the field and help cement my growing understanding of best proteomic practices. I felt very alone and new to this crowd, with only one or two familiar faces in 240 delegates. However, I was lucky to be a speaker selected from abstract (a fancy way of saying I applied with a description of my research, and they chose me as one of the ~60 presenters). This was a true treat, as it was a great way to introduce myself and my work to a completely new network of scientists. I got some great feedback and a brand new approach to my project. What struck me most about this conference was the diversity of science that was covered in the talks. Being primarily a technique based conference (as opposed to a biological theme as with the Proteins meeting), there were marine biologists, physiologists, ‘method’ologists (mass spectrometry, crystallography, electron microscopy), molecular biologists, statisticians and mathematicians. It was a great overview of the scope of disciplines in which proteomics and associated techniques are both indispensable and actively developed.

An interesting side-note to this conference was the inclusion of the Annual General Meeting for the Australasian Society of Proteomics. This was my first foray into Society politics and management. It was a really great opportunity to observe the inner workings of the society and see where I could potentially get involved in the future. There were rumblings of an ECR-led program for Lorne Proteomics 2020, so stay tuned!

Barely a few hours after the close of the Proteomics meeting, the Proteins delegates descended on Lorne. The faces were more familiar and, for someone who enjoys the sensation of routine, everything felt a little more like ‘home’. The first night featured one of my favourite sessions - the Leach lecture, in which an emminent Australian Protein Scientist is awarded the lecture and intertwines personal experience with scientific detail. This year’s lecture was given by Ray Norton, and he did not disappoint.

Ray Norton on his journey, quoting John Lennon (or more accurately Readers Digest!)

“Life’s what happens when you’re busy making plans”

— Dezerae Cox (@dezeraecox)

Other notable sessions included the Student & Invited Speaker lunch, where I was a ‘facilitator’ (my job was to help stimulate conversation across the table). As well as the great opportunity students had to interact with our international visitors, there were two keynote speakers. First, Liz Miller gave a great summary of her science journey - how she had landed in her first post-doc, managed to coordinate two academic careers across the globe, and how she had taken advantage of the often serendipitous nature of science. Her take home message was planning moves in science takes time, so start looking and thinking about it early. This was echoed by Nobel Laureate Richard Henderson, whose take-home message was to do almost as much research into the paths you can take, and the places you can go, as actual science itself. I think, in our current scientific and political climate, that these messages could not be more timely for students to hear from leaders in our field.

Last but not least, I had the chance to catch up one-on-one with two of the international speakers. Building on my confidence from the Proteostais and Disease Symposium, I took this opportunity to get their input on my current project, their thoughts on my career goals and their advice on moving forward over the next few years. I am truly amazed, and incredibly grateful, for the generosity of experienced researchers in offering their mentorship to me as a young Early-Career Researcher - it turns out that sometimes all you have to do is ask.

It goes without saying, that if you ever have the chance to get to one of the Lorne Conferences you wont be disappointed. Hopefully I’ll see you there next year!

Advanced Scientific Programming in Python Summer School

Thu, 25 Jan 2018 23:10:08 +0000

Another post, another conference!

This time it was the Asia-Pacific “ . A full 6 days of intensive training in the programming language Python, designed to extend my amateur skills and give me more tools to analyse my data.

And boy, did it deliver - kicking off with some free swag!

The formal sessions started with a welcome from the school’s founder, Tiziano, who’s first iteration of the school was over a decade ago. His opening remarks really resonated with me:

In industry there are normally teams tackling a problem. and it is important to be kind to your teammates by writing nice code and documenting well. In science, we often work alone on our own data, and that teammate is your future self. This week is all about being kind to your future self.

Each of the main sessions targeted a specific element of scientific program in python (from GitHub to tidy data in pandas to plotting with MatPlotLib to parallelization to packaging to cython). The tutors would spend a few minutes making sure our basic knowledge was up to speed, before taking those concepts and extending them beyond what I had ever considered possible from my programming life!

A huge part of the success of the school was pair programming. The school provided one computer between two, all formatted identically and containing all the necessary applications for the week, with which we were to work in pairs to solve the lecturer’s exercises. This was a completely new experience for me - not only had I never worked with anyone else collaboratively in a coding environment, I was not accustomed to sharing my code with anyone! I have always been shy of sharing my programs, feeling like they were amateur and ‘half done’. Now, not only did my partner get to see the ‘final’ product, they would get to watch my thoughts take shape on the page! As terrifying as it sounds, I really did learn a lot from observing others and from their input as we worked together.

To consolidate our knowledge, on the final day we were split into teams where we would collaborate using our newly minted GitHub skills. The goal was to program two pacman bots which would be pitted against the other teams in a tournament - not only did I have a great team, and a great time learning to work with the bots, but we WON! This meant the delivery of swag #2: a signed copy of “Elegant Scipy”!

With tutors from Europe, New Zealand, South America and Australia, we were spoilt for expertise. Most surprisingly (and delightfully) of all was that the student profiles were just as diverse! Over the course of the conference, I worked with a particle physicist, a plant biologist, an engineer, a medical radiation physicist and a virologist. Not to mention the age, cultural and gender diversity - the group of students was a beautiful reflection of the diversity of the scientific community.

I can honestly say I felt so privileged to be selected (the conference was free to a limited number of students), and it was hands down the most practical and valuable conference for developing skills I have ever attended. If you ever have the chance to go, I cannot recommend it enough.

Happy programming!

ideas on what helps and hinders symposium speakers

Mon, 27 Nov 2017 20:28:25 +0000

During the recent , a friend was scheduled to give a talk about her work. Sitting in the audience watching a parade of marvellous speakers is a special kind of torture, when you are convinced you could not possibly achieve a similar performance. I should know - until the very last year of my PhD, I was not a very talented communicator either. However, after a venture overseas and a stint in a different lab, I found my voice. I wouldn’t say I’m brilliant (far from it), but I have realised the importance of this aspect of science communication and worked hard at being able to at least stomach the idea.

My friend asked how I’d done it. How do you overcome the paralysing fear most people associate with public speaking? I didn’t really have an answer for her at the time - I encouraged her to be confident, which is of course the main ingredient. However, I have thought about it since then, and while watching the remaining conference talks I came across a few things that as an audience member I think can make or break a presentation.

1. Don’t repeat your talk name and title - people can read the program and your first slide (we are mostly smart cookies after all), and it is the job of a good session to chair (also presumably a smart cookie) to give those details when they introduce you. Instead, open by thanking the organisers for the opportunity to present some exciting new work, and a one line teaser to grab the audience - tell them why they should pay attention RIGHT NOW, and not wait until five minutes into your talk. If you don’t have them at the beginning, there will be no getting them back.

2. Oh, you’re skipping your introduction? Because EVERYONE ELSE has given this intro? At a conference specifically about your topic? NO WAY?! Think about your audience early on in the talk’s preparation stage and don’t be afraid to adjust on Day 1 of a three day event. If available, check out the program/other abstracts early, highlight talks with relevance to yours and gauge the level of any remaining introduction that you will need to give. Being able to refer to someone else’s intro not only shows you have engaged with the symposium but also gives you more time to go through the exciting bits (your results!)

3. Keep it simple, stupid. Most of the time you will have a very short window in which to convey your story, which will inevitably be the result of months and months of your blood, sweat and tears. Trying to cram too much into this time window makes your story confusing and hard to follow (10 tiny bar graphs on one slide, anyone?) and people will loose interest. Focus on a simple message, tell people what they need to understand that message, tell them what the message is, then reiterate why your message is important. Simple. As a bonus, people will chase down details with questions, avoiding the dreaded crickets-and-tumbleweeds at the end of a particularly confusing or dense talk.

4. Following on from this, constantly telling people you don’t have time to present this, that or the other (in an effort to keep the slides simple), sounds arrogant and selfish - figure out a story that you CAN tell in the allocated time and reiterate that you are happy to talk details during the breaks.

5. Fake it till you make it. This one has stood the test of time, and for good reason. So much of our perception of a good presenter is taken from their physical cues - and that stems entirely from confidence. If you are nervous beyond belief and terrified of doing something wrong, that will inevitably come through in your body language. If you own your talk and your work, that will come across instead. I think of this like you are the pilot of a plane - if you sound scared and uncertain, your passengers are going to be unsettled and anxious, leading to this cycle of negative reinforcement. If instead you get on the PA system, calmly detail the weather or flight plan (how would they really know how high you’re going to fly??) and make them believe you are in control of the situation, your passengers (the audience) will be calm and the atmosphere relaxed. Everyone will make it out alive and live happily ever after. Or so we hope.

Got any good tips that I’ve missed? Let me know your secret ingredient!

Proteostasis & Disease Symposium 2017

Mon, 27 Nov 2017 09:55:59 +0000

The last week saw me spend more time speaking than I can recall in recent memory, all thanks to the . A blur of yummy food, wonderful people, stunning views and cutting edge science - all the makings of a good conference. If you don’t believe me, you can see what others thought here:

There are many, many meetings of scientists all over the world scattered throughout the year, but this particular conference will always have a soft spot in my heart. It is in my hometown (the absolutely stunning Wollongong), hosted by my alma-mater, and is the perfect way to showcase my science, show off my old stomping ground to international guests and catch up with my scientific family.

There was a good mix of invited international speakers, presentations selected from abstract submissions and poster presentations from PhD students at various stages. All of the talks described essential research techniques and reported positive outcomes. Truly inspiring talks that fired up my brain with new and interesting ideas, drawing spiderwebs of connections and blossoming collaborative projects.

This is part of the reason why I really enjoy scientific conferences. These opportunities are a great time to take stock of my own research and think more about how it fits within the wider field. Often, scientific research can be draining. A mass of rejections, failed experiments and job insecurity can make it difficult to remember why it was I chose this path in the first place. However, conferences are a way to reinvigorate my scientific curiosity, and many times have been the cure to a significant slump.

I mentioned that I spent a great deal of the conference talking. Having moved away at the beginning of the year, this conference was my first opportunity to catch up with people from my old institute. More importantly, though, I made a conscious decision to gain as much as I could from the three day event by focusing on my networking skills. I was determined to move on from being the shy PhD student hoping to fade into the background, and made it my mission to engage with the international guests of various levels at every opportunity.

I was lucky enough to spend a significant amount of time chatting with two of the senior researchers. I can honestly say, although at times terrifying, that this was one of the most rewarding experiences of my career so far. Despite being ‘celebrities’ of the field, they were extremely personable and made for engaging dinner conversations. More than that, they were both forthcoming with experience and advice, and offered carefully considered critiques of my research.

For those lucky enough to be blessed with the self-confidence to be unfazed by encounters with important mentors, this may not seem like a big deal. I can assure you, for me and many others, it takes a vast amount of courage and persistence - but the reward is also much much more satisfying. Feeling as though you have made a new connection with a likeminded peer or professor in your field is truly an accomplishment. Knowing that you are able to achieve something you set your mind to has a funny way of boosting your confidence, and an even funnier collection of flow-on effects.

Returning home, I am happy and excited for the week ahead. Armed with my new-found confidence and three potential new collaborations, tomorrow is the start of one of few weeks left in the year. I don’t know about you, but I’m going to make the most of it!