Come work with us – two positions as post doctoral fellows in disease ecology are available

Funding comes and goes in mysterious ways, but right now I am in the fortunate position to advertise not one, but two postdoc fellowships in disease ecology at the Zoonotic Ecology and Epidemiology lab at Linnaeus University in Sweden. This is a great time to come join us! The lab currently consists of two senior researchers, four postdocs, two PhD students and one technician. We are also part of the centre of excellence Ecology and Evolution in Microbial Model Systems, a body of 50 or so researchers (PIs, postdocs, PhDs) that collaborate at the crossroads of disciplines. You will have a great time!

The project

The influenza A virus is a multihost pathogen with zoonotic potential, but most subtypes and genotypes are associated with wild birds, in particular dabbling ducks of the genus Anas. Since 2002, the Zoonotic Ecology and Epidemiology research group has worked broadly on host-pathogen interactions of this virus in a population of migratory Mallards in SE Sweden. Through systematic sampling for viruses we have built up a large collection of influenza A virus, and combined data on host and virus to build infection histories of the individual ducks. These data, together with targeted studies on movement ecology of Mallards, have enabled us to address disease ecology questions in this system. Currently, we seek to strengthen our research team with one or two Post Doctoral student(s) interested in disease ecology of IAV in a broad sense. The interested student should have research interests and prior experiences that align with the currently ongoing research, but could be focused either on evolutionary aspects of the virus (phylogenetics and evolution, or functional aspects of virus), or the consequences of the host of infection (either in terms of ecological costs, epidemiological modelling, or disease in a movement ecology perspective).

Qualifications

Requirements for the position are a strong record of disease ecology research with a PhD in either virology, veterinary medicine, ecology, molecular biology or similar. Other assessment grounds that would place the candidate at an advantage include a presentation of documented evidence of disease ecology research, preferably on influenza A virus, a high proficiency in written and spoken English, the ability to solve problems and to work independently, as well as interact in a research group.

Terms of employment

The position will be full time for 2 years. The proposed starting date is from the 1st of January 2017, but can be negotiated.

Apply?

Find out more and file your application on the following link.

Want to know more?

Check out our blog, read our papers, or send me a direct email (and to prove you are not a robot: jonas dot waldenstrom at lnu dot se)

Happy duck trap day!

Yesterday, while fiddling around with some data for a government report I realized it was exactly fourteen years ago we opened the doors to the duck trap at Ottenby and started our surveillence program of influenza A virus in waterfowl. Fourteen years – and our fifteenth autumn season! That’s pretty good for a field series in ecology, and very, very good for influenza A virus surveillance in wild birds.

So happy duck trap day to all of you duck trappers (many, many), students (four PhD students, a good number of master- and undergraduate students), postdocs (four postdocs) and collaborators (from Sweden, The Netherlands, Germany, France, UK, US, Chile and elsewhere) – without you this wouldn’t been possible. And a big thanks to various funding agencies for supporting this work along the road.

Time flies, and so does the birds – and the viruses.

Memories of stromatolites

Some twenty plus years ago, I attended my very first lecture at Uppsala University. It was a strange mix of anxiety and anticipation that flooded through me as I went up the stairs to the theatre on the top of the Zoology building. Although I was certain that I wanted to study biology, I had no clue as to what university studies really were. It turned out they were a bit scary, at first.

As the lecture room had filled up and the lights dimmed, a guest professor spent the next hour speeding through a fact specked presentation in accented English and with PowerPoint slides in Spanish. I think he was pretty famous in his field, but it was somewhat wasted on us as most had never listened to a lecture in English before, let alone had any prior knowledge on the beauty of fossilized bacterial stromatolites. But as the days went pass, turned into weeks and later months and years, my interest in biology grew steady from that point, fueled by a series of great lecturers and by friends that shared my passion.

Yesterday I was back at my Alma Mater for a thesis defense, climbed the same set of stairs and entered the room that once was so intimidating. Funny, though, it was much smaller than I remembered it to be; just an ordinary medium sized lecture room. And not a single stromatolite to be seen.

Bavarian farmers and avian immunology

I spent most of last week enjoying the warm autumn weather at the Bavarian Farmers’ Association meeting venue in the little town Herrsching, an hour’s train ride outside Munich. And no, I have not become a farmer, and definitely not a Bavarian farmer – the reason I went there was to visit the biannual workshop of the Avian Immunology Research Group and learn more on the intricacies of birds’ immune systems. And when I say birds I actually mean chickens, as the ancestors of the little Red Junglefowl is the avian version of the mouse model and one of the world’s most important protein sources.

It was a fabulously well-organized meeting, bringing together around 150 or so scientists. Lots of immunology stuff. Lots of advanced immunology stuff, to be honest – way more advanced than that I and my eco-immunology friends do. Actually, this was the main message I brought home: that we ecologists have so much to learn from the immunology people, and vice versa.

In our duck research, we dabble with immunology a bit – but the tools offered in chicken immunology are not yet available to us. There were beautiful slides with immunohistochemistry, tables with cell counts based on flow cytometry, immortal and primary cell lines, antibodies of all kinds, protein structures, custom made inbred chicken lines (including the MacRed breed), and widespread use of transcriptomics, genomics and whatnotomics. It was truly amazing.

Starting as avian ecologist and later branching out into disease ecology I have over the years attended many bacteriology and virology conferences. The one thing that always strikes me is how little conference jumping there is. Ecologists tend to go to ecology conferences (which there are many, with varying degree of specialization), virologists go to virology meetings, campylobacter folks go to campylobacter meetings, and so on and so forth. Partly this is because of different training and research interests, but perhaps it is also partly because of old habits, where the prospects of meeting up with old friends and colleagues is as strong an incentive as the actual science part of the conference.

As a satellite meeting, the duck crowd met up and spent an extra day discussing where to head next in duck immunology. And there is loads of cool stuff we can do, and that we hope to do. Especially if we get more funding.

Needless to say, I had a great time, and even drank a few German beers and dined on knödel and schnitzel – as one should. Back in the lab I have to deal with the backlog of emails and manuscript, but science wise I feel ready to level up my immunology branch of duck disease ecology. In fact, in a week or two I will write a piece on our upcoming innate immune paper on Mallards. Stay tuned.

What lies ahead post-Brexit?

 

A fridge magnet my daughter uses to tell that ‘she isn’t here’. The question is what fridge magnet we should use for science post-Brexit.

As all of you know, UK voted for Brexit.

In the local village sauna (yes, we have one of those) the reactions ranged from Brexit being stupidity in action, to quotes such as this was EU’s fault for not being on par with the people and that this could serve as a bloody needed wakeup call for the union. I sat mainly silent, stunned by the absoluteness of the decision. Because it is such a major decision, and a decision that have ramifications on so many levels for so many people.

As a scientist, I wonder what this will mean for UK and EU science? Truth is, no one knows. (And the elderly men in my sauna had no answer either). What we do know is that over the years, science and education have become more and more interconnected in the EU as a whole. And that’s a damn good thing. During my career it has become easier to study and conduct research outside Sweden, and for students from other countries to come to Sweden. Actually, after finishing a PhD, one of the most common ways of continuing in science is to apply for EU-funded postdocs (foremost via the Marie Skłodowska-Curie grant programs). I have many friends that have done that journey, and as PI I have had students applying for this funding to come to my lab. Also at the next level, where an aspiring scientist wants to develop his own research group, the EU provides means to do so via the ERC starting grants. Will these opportunities remain for young UK researchers? And what will happen with the opportunities for postdocs from the rest of the EU to do their work in the UK? The UK has been a magnet for talented Europeans for a long time, and it would be a terrible loss if that door, if not closed totally, would be harder to get through. Moreover, what will happen with European-wide calls, such as Horizon 2020 grants? At the moment I am participating on a grant proposal at the second stage where 2 out of the 6 partners are from the UK – will it be considered for funding anyway?

The interconnected science world is manifested also locally, even in a small university such as the one I work at. For instance, I have participated in EU-funded research, acted as an expert in EFSA (European Food Safety Authority) opinions, have had UK colleagues on shared grants, hosted postdocs with roots or training in the UK, and once I was close to actually move to the UK myself. I have met so many talented UK researchers at so many different levels. It is a shame if the ties connecting research between UK and EU will be weakened. It would be a great loss for EU and devastating for the upcoming research generation in the UK if they cannot participate at the same level as other European researchers.

You may say that is doom and gloom talk, that in fact not much will change, that either EU or the UK will make sure that funding and research opportunities will continue more or less as they are now. I hope you are right, but fear that you are wrong. For sure, there will be a backlash if article 50 is invoked, the question is how big and how long-lasting it will be. Because once you’re out, you cannot really continue business as usual. Simply put, why would EU-funds be used to support UK research and infrastructure in the future if not the UK is paying their share, or if EU-researchers cannot move freely to the UK?

It is still early on in the Brexit process, and we’ll have to wait and see what will come out of this mess. If my crowd in the sauna come up with a solution, I will let you know.

On the cover

In the Swedish academic system a PhD thesis is an actual printed book. Yes, a proper book-looking book. A kind of book you can shove in the hands of your family and say ‘here it is, the fruits of my labor, the sum of all my forsaken years, MY THESIS!’

The editions are small, usually between 100 and 200 copies, of which 30 go to specified libraries, kept safe in the hallways of science. One is nailed to an oak tree three weeks before the thesis defense, thereby symbolically presented to the public (and continuing a tradition dating back to Martin Luther’s nailed thesis to the church port of Wittenberg in 1517). Although it probably isn’t really necessary to print them on paper in this age of computers, it is a tradition worth honoring. More than anything it represents a closure of sorts, and a mark of something new.

I really like that feeling when the book gets back from the printers and the student finally sees the end of the wonderful but torturous path that is a PhD. The making of the book is sometimes also an act of procrastination, where the student can spend an inordinate time adjusting the colors on the cover, rather than finalizing that final chapter.

Below are the theses produced in our research group in Kalmar the last years. If you want to read them there are links to the online publications too.

• Daniel Bengtsson, Linnaeus University, Stopover ecology of mallards – where, when and how to do what? 11 March 11 2015, ISBN 978-91-88357-00-7.

• Michelle Wille, Linnaeus University, Viruses on the wing: evolution and dynamics of influenza A virus in the Mallard reservoir, 8 May 2015. ISBN 978-91-87925-56-6.

• Johan Stedt, Linnaeus University, Wild birds as carriers of antibiotic resistant E. coli and Extended-Spectrum Beta-Lactamases, 13 June 2014. ISBN: 978-91-87427-93-0.

• Petra Griekspoor, Linnaeus University, Exploring the epidemiology and population structure of Campylobacter jejuni in humans, broilers and wild birds, 28 May 2013. ISBN 978-91-87427-83-1.

• Neus Latorre-Margalef, Linnaeus University, Ecology and epidemiology of influenza A virus in Mallards Anas platyrhynchos, 8 June 2012. ISBN 978-91-86983-61-1.

• Jorge Hernandez, Uppsala University, Human pathogens and antibiotic resistant bacteria in the Polar regions, 10 October 2014. ISBN 978-91-554-9016-4.

Jenny Olofsson, Uppsala University, Amoebae as hosts and vectors for spread of Campylobacter jejuni, 2015. ISBN: 978-91-554-9276-2.

Go, blog, go!

To run a blog is fun, but taxing. In order for it to fly you need to post new items fairly regularly and, of course, have something to say when you do. The Zoonotic Ecology and Epidemiology blog is primarily an outlet for communicating the science we do in our lab, but it also serves as a venue for me to tap away at the keyboard at those rare occasions when I’m in the inspiration zone. As such, the blog does not aspire to be ‘a voice’ for any defined grander cause, and the number of posts published is somewhat unpredictable. But I like the blog, and often think about posts that should be written.

The wordpress platform gives you loads of stats to boast or deflate your blogo-steem, as the number of page views summed on day, week, year, or from which countries blog visitors come from. You can even get hold of the search queries that directed searches to the site (and, man, those are sometimes weird). Thus, I can see which posts that get attention, and which do not. To be honest, I am fairly amazed with the 24,422 page views so far (as of five minutes ago). While this number is nothing compared to the big fish in the blog sea, it is a considerable larger number than the sum of my extended family and friends.

But what about wider splashes? Well, occasionally someone makes a comment on the blog, or make a pingback on another post elsewhere in the ecology/epidemiology blog community. That’s nice. And every now and then a colleague (either here or abroad) says something to me in person, which is nice too. However, the most direct consequence so far is an invitation to write a book chapter on Mallards and disease (which is coming, I promise…). Apart from that, blogging is mainly a one-man chorus in the desert, with rocks as audience.

But a few weeks ago something unexpected happen: an old post of mine was cited in an article in PLoS Biology. That’s pretty cool, I’d say! The post that was picked up was this one, on the data accessibility discussion triggered by the new guidelines at PLoS ONE – a topic that sparked some heavy blog fire on different sites. The perspective by Roche et al. asks how well we are doing in terms of data archiving in ecology and evolution – and the answer: not particularly well – and uses the blog discussions as an example on how scientist reacted to the new policies. We can now tick off ‘being cited’ on the blog bucket list.

So, go, blog, go! Someone is reading you!

Head lice – the unwanted gift that keeps on giving

Human head louse in close-up. [Photo by Flickr user Giles San Martin under a CC BY-SA 2.0 license].

There are two telltale signs that your kid’s class is infested with head lice (or in scientific prose Pediculus humanus subspecies capitis). First, and foremost, scout for kids that obsessively scratch the back of their heads – chances are they have a little colony of lice brewing. Second, as many treatment formulas contain oily substances, beware the greasy appearance of post-treatment hair. But most of the time you don’t need to be in doubt, as there is usually a sign on the school door saying ‘there are head lice around’. In my little town, and in Sweden in general, head lice are now a normal occurrence in the younger kids, and an unwelcome gift when the children gets back to school in autumn.

And once a school has them, it seems they are impossible to weed out. Head lice infestations still carry a social stigma, especially among the older generation. Head lice were more or less exterminated in Sweden in the 1950-1980s, and were thought to be restricted to poor people with limited access to sanitation. However, that’s not true anymore (or perhaps never was) – there are head lice climbing around the offspring of lawyers, bankers and…. ahem… professors. One reason for this re-emergence is evolved resistance to the compounds used to treat lice infestation, but likely our ever increasing busy lifestyle is to be blamed too, as effective treatment really only is doable with the painstakingly gruesome louse combing (which most little ones think is torture).

Contrary to most people, I think lice are fascinating critters – at least as long as they stay out of my hair. They are extremely adapted to their niche: the flowing hair of the human skull. Inside this jungle, the lice dart around fast as lightning from one end to the other, usually without us knowing it. However, if you catch one and put it on a flat surface you’ll see that it is unable to move, as the louse’s legs stretches horizontally, adapted to efficiently grab hairs, rather than strolling around. You can also see whether they have fed or not, and from that gather whether a new generation of lice are being produced.

Furthermore, consider the boom and bust dynamics that goes on day after day at the louse population level. Each human head is an isolated patch of habitat, and migration to other patches dependent on the behavior of the host – when we hug each other, swap caps, or in other ways put our hair together – behaviors that differ dependent on age class and gender of the host. For example, in my thinning hair, the poor lice have limited chance of long-term survival (a windswept barren heath land, from a louse perspective), while in my youngest daughters the hair is long and interactions with other suitable hosts frequent. Even so, most colonizations of a patch are likely to involve only a single or a few lice, from which a new generation need to stem. Sexual reproduction is the norm, so either the adult female needs to fertilized before moving to a new host, or she has to have company of a male to start a new colony.

But when the population of lice increase, so does our likelihood to notice them. And once noticed, full war is waged in order to exterminate them. This involves various expensive shampoos, often containing substances that immobilize and suffocate the lice, and, of course, good ol’ fashioned combing. The effect is recurrent population bottlenecks, where numbers of lice go down to very low level before bouncing back. One wonders how they manage to avoid deleterious inbreeding effects.

It isn’t an easy life being louse, loathed and hated by their hosts – but it is the only life they know. Simply, lice are good at being lice, and are unlikely to ever (as in evolutionary times) leave their fitness landscape peak and abandon parasitic life. As for now, they are the unwanted gift that keeps on giving.

What do you do when you read a really poor scientific paper?

I read a poor paper the other day. Given the fact I read too few papers, I am always a bit annoyed spending time reading a bad one. I can live with a typo or two in a paper, but when authors are demonstrating limited grasp of the literature and are overselling the importance of their findings, you get kind of annoyed. Worse still when their data is crap and the analyses clearly weak.

So what do you do? Normally nothing, I suppose. It is not the first, nor the last bad paper I have read in my subject field. The normal cause of action is to drag it to the bin, and/or warn your students about it at a journal club. Thus, generally one just hopes it sifts to the bottom of the academic publishing ocean along with other poor papers no one will ever cite.

However, in this case, I wrote a rant aimed for this blog, pointing out the various things I disliked with the paper. A quite annoyed and detailed rant. But before pushing the publish button I changed my mind, as slamming down on a paper too hard is a bit of a bullying behavior. And I rather see the science improve than shaming the scientists.

The problem here (e.g. the poor paper) could have resulted from one or several factors: a poor manuscript submitted to a mega-journal, non-expert staff assigning an editor, this editor accepting a manuscript outside his main research field, unqualified reviewers reading it, the authors not paying attention to reviewers’ concerns during revision, and the editor accepting a paper with outstanding issues.

As for quality, the editor is always the gatekeeper, regardless if the journal is highly selective or do not make decisions based on perceived impact. The science needs to be sound, end of story. If not, the study should be rejected, or shaped by rounds of revisions until it is suitable for publication. Being an editor for this journal too, I contacted the journal office and told that my fellow editor most likely is unsuitable for his position and asked they make an investigation. We’ll see what they say, in the end. Ultimately the fate of a journal is based on the quality and rigor of review, so I am sure they will react accordingly.

Grinding the crack – contemplating on rejection times

Our minimum NRT at the time of writing.

Science is slow and tedious. And that is how it should be. There is a beauty to behold in the accumulated data points in supplementary files and appendixes. A life worth of time, poured into tables. Neatly ordered references with doi numbers. Ordnung.

However, at times science is also dead fast. Try the last months of your PhD, for instance – that time just is surreal. But the fastest of all is NRT – the average timespan between the click on the button on Nature’s submission form to the email back in your inbox with a rejection letter. Most senior scientists I know have tried at least once to publish in Nature or Science, the two most famous journals across disciplines.

Most of them without success.

This makes for great conversation, and it is common to hear people telling stories of their NRT. Our record is 2 hours. TWO HOURS! Damn, that’s fast. A friend of a friend apparently was rejected within 22 minutes. That’s impressive!

At present we are up at 27 hours, 11 minutes and 31 seconds. Pretty good – at least we joke about it in the little cohort of authors. This likely means it will be read properly by an Editor, and hopefully make it out on review.

And if it doesn’t cut it for Nature, I am sure it will find a good home elsewhere – it is a very nice piece of work that taken us 3 years to analyze.

Meanwhile, enjoy Jeb Corlis in his Grinding the crack video. It summarizes the processes of publishing in top-notch journals better than any words could.

Just click it.

For you, Jo.

Cheers.

*************************UPDATE*************************

The final NRT for our manuscript was 49:30:21,92. Something to beat next time. Now this little baby needs to find another journal home