The story behind the paper

We recently published a paper on genomic surveillance of a diarrhoeal pathogen Shigella sonnei across Latin America which represented the culmination of over five years of collaboration, as well as training and development in the region

Graphical abstract

In collaboration with the Wellcome Trust Sanger Institute, the Pan American Health Organisation and PulseNet Latin America and Caribbean (PNLAC), we whole genome sequenced over 400 Shigella sonnei collected from nine countries over two decades. Shigella are the most important bacterial cause of moderate-to-severe childhood diarrhoeal disease in low to middle income nations, and countries in Latin America still experience endemic disease and explosive outbreaks. By sharing information on common pathogen subtypes through public health networks, like PNLAC, pathogens can be traced epidemiologically to facilitate early identification and intervention in disease outbreaks. Whole genome sequencing is transforming surveillance of bacterial pathogens, as it provides the highest resolution of pathogens subtypes and can also be used to explore other genetic factors of interest, like antimicrobial resistance. However, its cost precludes routine use in some areas, which are unfortunately some of those regions where the most Shigella disease is seen.

In this study, we sequenced approximately 50 isolates from nine countries in Latin America and use whole genome phylogenetics to reveal those sublineages that were responsible for most of the disease in the region. We identified a novel global lineage of Shigella sonnei, and by correlating the geography of where isolates came from to their evolutionary relationships, we could see international transmission of some sublineages and what the distribution of different sublineages was across the continent. Visit the microreact page to play with the data yourself.

We were also able to identify key determinants of antimicrobial resistance in the pathogens and how they were distributed among the different sublineages, providing key information for managing this important disease in the region.

In addition to constructing this invaluable regional framework for ongoing surveillance, this project helped build capacity for whole genome sequencing surveillance in the region. Over the course of the collaboration, the World Health Organisation sponsored the establishment of whole genome sequencing facility at the reference laboratory for PNLAC, ANLIS in Buenos Aires, Argentina (see photo). In the paper, we show how locally-generated sequencing data from this facility can be integrated into the regional surveillance framework to determine whether outbreaks were due to locally-circulating lineages or resulted from the importation of new sublineages.

In addition to laboratory capacity building, the collaboration involved training an ANLIS researcher (Josefina Campos – see photo – who now runs the genomics facility there) in bioinformatics, and conducting training courses (in conjunction with Wellcome Trust Advanced Courses) for medical, veterinary and public health professionals in the region, including courses in Argentina, Uruguay and Costa Rica (see picture).

There are 29 authors on our paper and every one of them worked hard on, and cared deeply about, the outcome of the study as well as the training programs and capacity building surrounding it. Every paper has a story behind it, and this one, like so many others, is so much more than it appears.

Photo: Top ANLIS in Buenos Aires, Argentina. Bottom (from right to left) ANLIS collaborator Josefina Campos and co-corresponding author Nicholas Thomson (WTSI) outside the Malbran (ANLIS) Institute; Genomics for Epidemiology and Surveillance of Bacterial Pathogens course instructors and participants held in February 2015 in San Jose, Costa Rica; co-corresponding author Kate Baker with bust of Carlos Gregorio Malbran, the ANLIS institute’s namesake.

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Grasslands at Ness Family Science Fair

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Raj Whitlock and PhD student Di Yang took part in the Ness Family Science Fair for British Science Week in March. They manned a stall with model grassland communities, and talked with members of the public about the importance of plants, how plants work, grasslands, their conservation and threats to plants from climate change. Their installation at the science fair also included a grassland-inspired arts area, which became a popular relaxation point for parents and kids in the hustle and bustle of the event (which was attended by ~1500 people).

Pint of Science – The evolution of feet, the brain and masturbation

Dr Rebecca Jones board picturefrom the School of Life Sciences recently hosted the Pint of Science event on evolution recently at the Shipping Forecast. Here’s what she had to say:

When I was asked to host a night for the recent Pint of Science event in Liverpool I jumped at the chance. I’d been to a couple already, Manchester and Exeter, and thoroughly enjoyed them. Pint of Science aims to bring science to local pubs where the public can listen to researchers describing their work. There’s normally a theme for each city, with Liverpool covering Our Body, Beautiful Mind and Atoms to Galaxies. As a lecturer in the School of Life Sciences I was hosting the ‘Evolution of feet, the brain and masturbation’ at the Shipping Forecast on the 15th May.

Alongside a team of volunteers (Georgia Drew, Amy Eacock, Chloe Heys and Jo Griffin) and a willing photographer for the evening (Lukasz Lukomski), we had our evening planned. As the public entered the venue, the basement of the Shipping Forecast, they had a chance to fill in the three quizzes set by our three fantastic speakers in the hope of winning some Pint of Science prizes. These included matching the footprint to the nationality, guessing which brain belonged to which animal and pairing animal’s with their penises.

 

After the welcome and thanking of the sponsors, eLife, we started with our first talk by Dr Kris D’Aout on the evolution of the foot.

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Kris discussed his work examining locomotion and the use of shoes in various countries, particularly India. Although it seems Kris struggles with volunteers here in the UK!

 

He even showed a video of a robot having to meander around some walking humans! Kris was met with a barrage of questions from the audience, including some asking advice on wearing slippers around the house!

 

Next up we had Dr Tom Butts who spoke on the evolution of the brain and he even managed to rope in some keen volunteers to demonstrate the formation of the spinal cord.

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Tom then received some rather tough and philosophical questions about brain development and dinosaurs which got everyone thinking!

 

We then had a break in which people replenished their drinks but also got to listen to three excellent 2 minute talks from researchers. Jennifer Mitchell, Elinor Chapman and Angela Hackett (L to R) all described their research without the use of props or slides to an enthralled audience who eventually voted Elinor the winner!

 

Our final talk, and headline act, was Dr Tom Price who spoke about the evolution of masturbation across animal groups.

 

Tom mostly spoke about sex and masturbation in birds although had some interesting theories on whether masturbation occurred in dinosaurs!! Tom said, “People seemed to enjoy my speculations on solo sexual behaviour in ducks and dinosaurs.” However, he was more surprised that “Some members of the public were surprisingly good at identifying weird animal genitals.”

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Following some entertaining questions and prize giving, the conversations moved upstairs where people were keen to find out more about feet, the brain and most importantly, masturbation.

I’d like to say thank you to the speakers and all the volunteers that helped on the night! There was a lot of organising but it made for a memorable event!

Mole rats without oxygen, seal necroscopy, and teaching teachers

  1. New Teacher Subject Day, Organised by the Prince’s Teaching Institute, Pimlico Academy, Saturday 14th January 2017

On Saturday, 14th January 2017, IIB researcher Dr Michael Berenbrink has been taking part in the New Teacher Subject Day organised by the Prince’s Teaching Institute (http://www.princes-ti.org.uk/). The event took place at Pimlico Academy School, London, where Dr Berenbrink presented a talk about his work on the diving capacity of marine mammals to 20 newly qualified and trainee school teachers for Biology. The Prince’s Teaching Institute is a charity whose mission includes to ‘invigorate headteachers’ passion for education, re-awaken teachers’ love of their subject, and show the newly qualified how to enhance their impact.’ Providing a wealth of resources, the New Teacher subject days are delivered by experienced teacher leaders in conjunction with leading academics and are designed to improve confidence and bolster ability.

 

  1. Symposium of the Liverpool Veterinary Zoology Student Society

On the weekend of March 25-26th IIB researcher Dr Michael Berenbrink took part in a seal necropsy and presented a 50 min talk on the “Evolution of oxygen stores and mammalian diving capacity –  from water shrew to blue whale” at the Northern Zoological Symposium in Liverpool, a multi university event with the aim to educate about all aspects zoological. This year’s event was organised by the Liverpool University Veterinary Zoological Society and included a series of lectures and practical sessions and a formal gala dinner at the Albert Dock.

 

  1. CNN Digital Commentary of naked mole rat study

On Friday 21st April, IIB researcher Dr Michael Berenbrink was interviewed by the news channel CNN Digital for his professional opinion on a study published in the magazine Science about the extreme ability of naked mole rats to survive without oxygen. The full report about the study including Dr Berenbrink’s comment can be followed here: http://edition.cnn.com/2017/04/21/health/naked-mole-rats-oxygen-study/

Family Science Fair at Ness Gardens, 11th March 2017

Iain Young and Laurence Anderson were talking to visitors to the Family Science Fair about Aquaponics today.

Laurence’s PhD springs from our partnership with Farm Urban www.farmurban.co.uk: an SME founded by two University of Liverpool PhD Graduates: Paul Myers and Jens Thomas. Paul Myers (winner of the 2016 Duke of York Young Entrepreneur prize) said: “Farm Urban take science fresh from the lab and implements it in aquaponics systems in the heart of Liverpool”. “The partnership between Farm Urban and the University of Liverpool helps us to develop and test the most efficient ways to grow food in urban environments”.

Aquaponics provides a focus for inspiration and a narrative for healthy eating and environmentally sensitive food production, which we have used to engage schools, residents’ associations, hospitals and other universities and to develop education and research around sustainable urban living.

Laurence Anderson brings aquaculture and plant growth trial experience from the recent BiFFiO (testing the potential of aquaculture and agriculture waste streams for biogas production and fertilizer: www.BiFFiO.com) and RAZONE (using ozone to improve aquaculture water quality: www.Razone.no) projects.

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Thoughts on #LiveTweeting

As a part of the Centre for Cell Imaging and a member of the Microscopy and BioImage Analysis community, I occasionally get away to conferences like the recent NEUBIAS training school and symposium in Portugal.

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Since having joined Twitter last year (@dn_mason), this is the second conference that I’ve been to, and as a result, was the second time I tried (with reasonable success) to Live Tweet at the conference.

Live What Now?

Going right back to basics, Twitter is a platform for broadcasting small messages (of ~140 characters). Some describe it as micro-blogging. To many, the brevity of each tweet is both it’s greatest strength and also one of the most frustrating features.

Live tweeting, is basically the act of providing a running commentary of a seminar, event or even a whole conference. All of the tweets associated with such an event can be tied together using a text-tag called a #hashtag (which starts with a hash like that last one).

You can always go back through the twitter website (or app) and see all of the tweets associated with a hashtag. For example, check out all the #NEUBIAS tweets.

OK, I get it, but why bother?

I find myself being asked this question quite a bit. So here are my three main reasons for live tweeting (in no particular order):

  1. OPEN NOTEBOOKS: Like most people these days, I have way too much paperwork. Between manuscripts, notes and admin, the last thing I need is more paper on my desk. By live tweeting, I can keep track of who presented what, and when (and, what I or the audience thought of that in the question periods/breaks). Once you get the hang of it, you can check and record links to papers and websites on the fly so you know that you’ve not made a mistake in writing down the the URL (especially important if your handwriting is less than clear). Everything is time-stamped and fully searchable so it’s easy to find that note you took six months ago (can you say the same about your regular notebooks?).
  2. ACCESSIBILITY: Plain and simple, live tweeting, gives people who aren’t at the event access to some of the ideas, thoughts and opinions that are expressed there (see endnote #1). Perhaps you’re off at another conference but want to stay abreast of the latest research, or maybe your budget doesn’t stretch to a trans-atlantic flight. Furthermore, this taps into the idea of open science. By sharing your ‘notes’ via Twitter, everyone gets interactive access to them and the community can start a conversation around them.
  3. NETWORKING: This might be a slightly broader point, but a lot of scientists use Twitter. By becoming part of the twitter ecosystem surrounding an event, you will probably find it easier to get yourself and your work known. You’re also becoming a bigger part of the community and getting involved with discussions to which you would otherwise be oblivious.

Tips for Tweeters

I am by no means a twitter expert (a twexpert?) least of all regarding live tweeting, but below are a few tips that might help you to get started:

1) Ditch the default website

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At least 3% of your screen here is taken up by beard.

The twitter homepage (above) may look nice but it’s really inefficient on space. Once you move to Tweetdeck, you will never look back. Tweetdeck is a very customisable app built into twitter. Compare the image above with the one below. Left to right, I have my home feed (tweets from people I follow), my notifications (people talking directly to me or interacting with my tweets) and the #NEUBIAS hashtag, all on one page.

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You can add as many columns as you want, so you can follow individual people, hashtags or direct messages, tailoring exactly what you see in each column (likes, retweets, follows &c)

2) Tabbed browsing

It’s fairly obvious that Twitter is a web application (see endnote #2). So you probably already have a web browser open. Learn how to use and manage tabbed browsing, so you can quickly search for websites (IE the speaker’s homepage), papers (PubMed or your equivalent repository), or relevant links that you might want to come back to later. Learn shortcuts to quickly switch between and close tabs.

3) Links and Hashtag

Does the speaker use twitter? If it’s not on their title slide, a quick search is a good way to find out:

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Assuming you don’t have a ridiculously common name…

If they do, include it in your tweet. It lets them know that people are discussing their work and opens up another avenue for discussion (once they’re off the stage).

This also helps with the visibility and networking mentioned above. Same idea goes for hashtags. If the event has a tag, use it in every tweet. Also, try to hashtag topics that will expose your tweet to others who might find the content interesting. #Don’t #over #do #it #though.

4) Harness the power of images

A tweet with an attached image is more visible and easier for you and others to find later when scrolling down a timeline. I try to add images at least once per logical break, even if they’re screen grabs from a website or company logos.

2017-02-18-tweets1Get to know how to screengrab, crop, save and upload an image quickly on your platform. Most browsers can open PDFs directly so you don’t need to download and open in an external application to screen grab an interesting figure or notable schematic from a paper. Make sure you include a link (a DOI or URL) so people can put the image in context.

5) Get to know the tweeps!

As I said before, a lot of scientists use Twitter. Try to figure out who are the people tweeting at a conference and make sure to follow them to see what they’re talking about. You may find extra insight or perhaps an interesting discussion point in which you can get involved (on or off-line).

The last word…

Live tweeting is not for everyone, but hopefully I’ve given you some reasons why you might at least want to follow a conference hashtag, even if you don’t contribute. Like any community however, the more people that get involved, the more everyone benefits.

 

ENDNOTES

#1: There is a really interesting discussion around this point, which extends to recording and/or streaming a conference. The argument goes that if people can “be at a conference” from their computer why would they ever pay the flight/hotel/conference fee to go to a conference in person? To me, this argument is patently ridiculous. Attending (most) conferences is about being part of a community, and this is a 2-way interaction. Some of the most interesting discussions happen over drinks or at meals, not necessarily during the talks and question periods. I’m fully for recording and streaming talks at conferences, and I seriously doubt that this would impact attendance.

#2: Many people use Twitter on their smart phones. The one and only time I do this is if I want to take a photo and tweet it directly. Otherwise, it’s just too slow and lacking in the editing / lookup tools (eg. good tabbed browsing) and screen real-estate to make the most of tweetdeck. If you can, always use a laptop or maybe (if you’re really good with it) a tablet.

Research in the Rainforest at Wolbachia 2016

Research in the Rainforest at Wolbachia 2016

Guest post by Georgia Drew (@GC_Drew), PhD student in the Institute of Integrative Biology, University of Liverpool 

Research in the Rainforest at Wolbachia 2016
28th June – 3rd July, 2016, Queensland, Australia

This year the beautiful Lamington National Park was home to the 9th International Wolbachia conference, a biennial meeting focusing on the reproductive parasite, Wolbachia, and other notable endosymbionts of arthropods and nematodes. Nestled in the sub-tropical rainforest, over 80 delegates from across the globe assembled to present work on the evolution, ecology, genomics and cell biology of symbioses.3-2

Mornings began with the bustle of bush turkeys and bower birds at breakfast, before full days of talks and posters set amongst the canopied hills of the park. Here I had the opportunity to present, at my first international conference, on the intriguing role of a symbiont, known as Arsenophonus, in honey bee colonies. Arsenophonus, just like Wolbachia, is a genus of bacteria that infects many Arthropod species. It is capable of a diverse range of interactions with different host species, from reproductive parasitism right through to nutrient provisioning.  My talk touched on the prevalence, transmission and phylogeny of Arsenophonus in UK bees and generated some interesting questions on the potential roles of Varroa mite and bacteriophage.

The reputation of Wolbachia as an adept manipulator of host biology attracts many to its associated phenotypes of feminisation, parthenogenesis and male killing – to name just a few. This year was no exception, with exciting reports of the discovery of new Wolbachia induced phenotypes, alongside the resolution of old ones. The genetic basis for cytoplasmic incompatibility (CI) appears to be finally unravelling with the identification of two Wolbachia prophage genes that induce CI like defects in Drosophila, while in Eurema butterflies there is increasing evidence Wolbachia can cause meiotic drive. Updates were also heard from the ‘Eliminate Dengue’ program, which uses Wolbachia infected mosquitoes to reduce vector competence for dengue virus. A bio control strategy that may also be deployable against Zika virus, and highlights the ability of symbiont research to resonate on a humanitarian level.

The conference was an exceptional opportunity to meet members of this relatively small field, and engage in discussion on many of the unresolved aspects of symbiont biology. Inspiration aside, the week was also incredibly useful for improving my understanding of an array of approaches and techniques that were showcased by speakers, some of which I look forward to transferring to my own work. As the conference came to a close, the more musically gifted among us performed a Beatles inspired tribute to Wolbachia – “we all live in a filarial nematode”, and I headed off to the east coast in search of kangaroos and humpback whales. I am very grateful to the Michael Pugh Thomas Fund and the Genetics Society, whose grants enabled my attendance at the conference.

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