Tom’s PhD at The Pirbright Institute

  
My name is Tom, I graduated from the University of Gloucestershire in 2014, with a degree in Biology. I have since been lucky enough to gain a PhD Studentship with The Pirbright Institute and DSTL on a project studying the role of genomic structure on the ability of viruses to adapt.

The Pirbright Institute is a world leading centre of diagnostics, surveillance and research of virus disease which infect livestock and which can be passed from animals to humans. The bulk of my PhD will be in the making of a number of RNA viruses in which the genomic sequences are changed while still encoding the same protein. These synonymous mutations will allow the role of translational kinetics on the co-translational folding and modification of the proteins to be assessed. As there may be an adaptive mechanism to control the rate of translation at specific points along the RNA virus genome, facilitating co-translational modification, and this may represent a constraint on the variability which a RNA virus can acquire.I would not have this exciting opportunity to work at Pirbright and DSTL if I had not studied an undergraduate degree at the University of Gloucestershire. From the outset I really enjoyed the breadth of the course offered by UoG. Although the course may seem heavy on the big stuff, and I really enjoyed the content on ecology, animal behaviour, natural history and phylogeny, my interest developed in the small stuff, molecular and microbiology. The flexibility in the course allowed me to choose from a number of modules which were much more heavily microbiology based. I was fortunate enough to work on projects which Anne Goodenough, Bethan Stallwood and Sally Rogers had undertaken, another advantage when I was looking for a position after my degree. These included studying the microbial load of pied flycatchers and the methylation of cytosine residues in a possible CpG island in the promoter region of a gene analogous to B-NK, again in pied flycatchers. Both projects nicely linked the large scale ecology, which I found to be very interesting, with molecular biology which I found to be more and more fascinating. All of these modules and projects gave me plenty of core skills which are required if you want to go on to a more lab based, micro career, and have proven to be invaluable. During my time at UoG I was also lucky enough to gain a period of work experience with an alumnus at Public Health England, again this gave me the opportunity to develop skills as well as to see the day to day running of a lab and the diagnostic assays and the experiments which are carried within them. This has proven to be one of the most beneficial opportunities from my time at UoG.
To those that wish to pursue a career in microbiology, or any career, my advice would be… 

Take every opportunity that is presented to you and be proactive in finding opportunities. Ask about the possibility of placements anywhere that is relevant to the career that you want to pursue. Get involved in any projects that you would enjoy or provides you with the relevant skills. Although, if it is a career in microbiology you want to follow, not being proficient at these skills should not put you off applying for PhDs as training is provided to develop all of the required skills. It is the awareness of what the skills entail and a keen work ethic that is most required. As well as the academic work and the development of relevant practical skills, it is important to enjoy yourself and to develop a broad set of interests, this will help you greatly in interviews and once you have the PhD (or job) it will be invaluable in searching for a postdoc (gaining promotion or looking for another challenge).

If there is a job, PhD or Masters that you are interested in, apply for it, apply for everything that interests you. Use interviews as an opportunity to see if you would enjoy working with those that are interviewing you just as much as they are looking for the correct person for the job. It is a two way thing, it isn’t just you who has to impress. Also, do not think that you have to take the first position that is offered to you, make sure you take the position that you will enjoy the most.

Most of all, push yourself to get the best degree possible, all the staff at UoG are incredibly accessible and approachable, more so than at any other university, use this. Not only will you gain a good degree, you will also have a much more enjoyable time and it is the good degree and your proactive time at uni that will stand out most when talking to possible employers.

Tom Nicholson, BSc (Hons) Biology

Analysing owl pellets from Skomer Island

As part of our third year Avian Biology module, students analysed owl pellets from Skomer Island, South Wales. The pellets had been kindly collected in Autumn 2015
by the island wardens and given to Matt Wood.
In most cases, these were from a barn owl Tyto alba, apparently roosting in a disused chimney, which gave the pellets (and the lab!) a rather pleasant smoky smell. In common with many birds of prey, owls often consume whole prey items such as mice, voles and shrews and then regurgitate the indigestible parts of their meal, including hair and bones. By soaking a pellet and carefully pulling it apart, it is possible to identify the prey. The different mammal species are best identified by their lower jaw bones. Although small mammals are most common, it is possible to find birds, bats, amphibians and insect remains too. 
  Of the 15 barn owl pellets analysed, 14 contained field vole Microtus agrestis exclusively. In most cases this would not be unusual as it is one of the owls’ favourite foods. In this case, though, it was quite a surprising result… because there are no field voles on Skomer! This is good evidence that the barn owls were roosting on Skomer and foraging on the mainland, perhaps with only opportunistic hunting on the island itself. This agrees with previous analysis of Short-Eared Owls Asio flammeus by Skomer’s wardens (http://skomerisland.blogspot.co.uk/2015/03/winter-leaves-its-mark.html) and also previous dissertation projects by University of Gloucestershire students Emily Compton and Elle Daley on Short-Eared and Little Owls Athene noctua (stay tuned for their paper… in review!): Skomer’s owls range widely to forage off the island. Of the barn owl pellets, only one contained a mammal species actually resident on Skomer: a wood mouse Apodemus sylvaticus.

 
The 16th pellet was from a Short-Eared Owl, and held perhaps the biggest surprise seabird remains. Based on the size of the bone, the shape of the leg bones, and the feathers in the pellet, this is likely to be one of the many Manx shearwaters Puffinus puffinus found on Skomer, and more evidence of opportunistic hunting.  

This just shows the value of owl pellets: fascinating insights can be made into science and natural history questions, all within a module-based lab practical!

Anne Goodenough, Reader in Applied Ecology

Matt Wood, Senior Lecturer in Biosciences

Striding out with equine dissertation

  For my dissertation project, I chose to investigate how a rider can influence the movement of a horse; specifically how the position of the leg affects equine biomechanics. This sounds really complex but it basically means that I am studying the way in which a horse moves, such as its stride length, elevation and extension and flexion of muscle groups. Equestrianism is an expanding global market with billions of pounds being spent every year on maintaining the fitness and health of horses. Riders are often the primary cause of equine back problems so understanding the specific impacts on position in the saddle is crucial in the prevention and remediation of equine injuries.

I needed to film the movement of ridden horses so that I could digitally map any changes they displayed. I chose 15 fit and healthy horses and (after much begging and many favours) I recorded them at a walk and trot pace with their usual rider. I asked the riders to ride with both short stirrups and long stirrups, in order to change their leg position. Once I had the recorded footage the next step was to analyse the clips using Quintic® biomechanical analysis software. I mapped the movement of the horse’s legs to determine stride length and looked at angles of flexion in both the front and hind fetlocks as well as shoulder, head and neck angles. 

The initial results suggest that the fetlock shows greater flexion when the riders stirrups are shorter. There is also a clear correlation between stride length and stirrup length, with the horse extending more when the stirrups were shorter. Following on from this I am investigating further into the specific impact of stirrup length on equine limb extension and flexion; shoulder and neck extension and flexion and differences in velocity and pace.

I have really enjoyed the freedom and in-depth study that the dissertation project offers, building on the things I learned in the level 5 Equine Biology module. Conducting your own research around a topic that interests you is a fantastic experience and I feel that I have developed many skills that I could take forward into any future role or study.  

Lucy Murrell, BSc Animal Biology final year student

The American cockroach and me!

 

Dissertation projects are a central feature of our bioscience degrees, a great opportunity to work on your own research project with support from the lecturers and technicians. Here, Trev Boreham writes about his project on personality in… cockroaches?!

With the back end of my second year looming and talks of dissertation projects in the air it was time to decide what I wanted to do my project on. I knew that I wanted to undertake a laboratory experiment looking at animal behaviour, I just needed to decide which organism to use. This urge stemmed from the second year module ‘Animal Behaviour’ which we were able to do our own behavioural experiment. I studied cannibalism in the American cockroach which was insightful and interesting (it also occurs, not pleasant).

One year on and I am in the company of the American cockroach once more but this time it was their potential to possess differing personalities that captured my attention. The behaviours I am hoping to establish are the boldness or shyness of individuals and sexes consistent across time. To examine this, many hours have been spent in the laboratory timing exploration of the arena, time spent sheltered and time taken to flee the safety of their familiar homes. This is often a tedious process but necessary if I want to produce a sufficient amount of data to draw reliable conclusions from.

Along the way I have encountered the odd setback with my project which have needed consideration. With the support from my dissertation tutor Adam Hart we have been able to discuss and iron these issues out and progress forward. This assistance is second to none and just knowing that advice is at the end of an email really relieves a lot of pressure.

I currently have a few more weeks of data collection then I can really get my teeth into the results and discussion. I have discovered that starting my dissertation early has reduced the pressure coming into semester two with other assignment deadlines due around and close to my dissertation deadline.

The experience of undertaking a science project of this scale has been very rewarding so far and I am looking forward to the end product.

Trevor Boreham, BSc Biology final year student

Adam on Christmas University Challenge, BBC2 December 28th

There are some things you just have to say YES to…and when I got an email from the producers of University Challenge inviting me to represent the University of Sheffield (where I studied for my PhD) in the Christmas Special series YES was my immediate response!

Of course, after saying yes the horrible reality sunk in. I’m pretty good at shouting at the TV when University Challenge is on and I reckon I get a good hit-rate with the questions, but of course I rapidly started analyzing my “performance”:

  1. I tend to ignore or discount those I get wrong
  2. I tend to consider those I “knew” but couldn’t think of at the time as a success
  3. There’s no pressure of buzzing
  4. You’re not on national TV looking like an idiot

This analysis was slightly troubling…

Pretty soon my team was announced along with the fact that I would be captaining. This means that I have to convey the answers to the fearsome Paxman during the conferring rounds…so no pressure there. Team Sheffield included the football journalist Sid Lowe, architect Ruth Reed and novelist Nicci Gerrard, better known as one half of the thriller writer husband-wife team Nicci French. We exchanged a few nervous emails but pretty much realized that there was nothing we could do now to prepare. It’s obscure general knowledge – what could you revise?!

The fateful day arrived for our heat, which was shrouded in secrecy. We didn’t know who we’d be playing although some detective work on Twitter meant that I was pretty sure we were up against Aberdeen. And sure enough, it was a Sheffield/Aberdeen clash in the penultimate heat.

Filming took place at Media City in Salford and was running very smoothly. They’d already filmed two heats by the time we arrived. We met Aberdeen beforehand (leader of the Scottish Labour Party, Chief Scientist of FERA, DJ Nicky Campbell and the head of ITV Factual) and then got whisked off to make-up and a quick chat with Jeremy Paxman. It turns out he’s lovely when he’s not sitting in the quizmaster’s chair. Powder applied we were suddenly sitting in the famous chairs and Jeremy was asking us questions….gulp…cue the fastest-slowest 28 minutes of my life.

With only the 4 highest scoring, winning teams of the 14 assembled going through to the semi-finals, the pressure was on…To find out how we did in our heat, tune in on 28th December at 8pm on BBC2!

6.4 - Christmas University Challenge 2015 - Sheffield with Jeremy

Anne’s Autumnwatch Adventure

Well, it’s been a busy 24 hrs. On Tuesday morning, I headed up to Scotland to film with Lindsey Chapman on Autumnwatch Extra. This is a behind-the-scenes, in-depth, look at the major stories in the main show. I was on the show to talk about the #StarlingSurvey that we are running with the Royal Society of Biology.

After a 5.30 am alarm call, four trains and a taxi ride (plus a spot of impromptu running at Carlisle station that underlined just how hard it is to run in walking boots) I arrived at the amazing Wildfowl and Wetlands Trust Caerlaverock on the Solway Firth and met the BBC production crew.

What a lot of cables!

What a lot of cables!

What struck me first is the sheer scale of the operation: it is truly incredible! They must have 80+ people working on site, from presenters to camera and sound operators, directors, producers, tech-savvy live webcam operators, runners, fixers, lighting gurus, and cabling boffins. Oh, plus the web and media teams, catering unit and makeup artists.

Anne on Autumnwatch Extra

Anne on Autumnwatch Extra

I did a 25 minute feature with Lindsey Chapman on the what, where, how and why of starling murmurations. This was all done live and without rehearsal. I’ve done some filming before but this was the first time I had to juggle not only the information I was trying to impart but also direction of where to move, how long was left, and what the viewers were seeing at any one time (which was often still images or other film sequences).You can see the finished thing here http://www.bbc.co.uk/iplayer/episode/b06p58gf/autumnwatch-extra-2015-6-afternoon-03112015

The main show contained information on the survey, and the outline map of starling murmurations created by Rik from last year’s data (https://uglosbioscience.wordpress.com/murmuration-map/). A slight gaff by Chris Packham live on air meant that I was initially referred to as Dr Holly Goodhead, who was a character in the 007 film Moonraker! I’ve always wanted to be a Bond Girl, but I never thought of it happening this way… …at least it makes the survey memorable, I guess.

Anne on Autumnwatch Unsprung

Anne on Autumnwatch Unsprung

After the main show, it was straight into Unsprung, which again is recorded live. I was in the audience but primed and ready to answer audience questions should any come my way so couldn’t relax until the closing credits.

As I type this in Dumfries, where Tuesday has almost turned into Wednesday, I’m thinking back over the day and trying to pick out the best moment. Actually, this was something away from all the media glitz: I saw my first ever ring ouzel! It might seem odd to pick seeing a white-necked thrush as my highlight over and above appearing on live telly, dinner with the production crew, and chatting with the Autumnwatch presenters after the show, but once a birder, always a birder!

Please submit new records here – www.rsb.org.uk/starlingsurvey. To see locations of records from last year, please click the “murmuration map” at the top of the blog homescreen.

Anne Goodenough

Matt Wood at the World Seabird Conference in Cape Town

This week I’ve been in Cape Town for an international conference that brought together seabird scientists from across the world. Seabirds are excellent models for a diverse range of questions in ecology, behaviour and conservation; to name just a few of the remarkable range of work that was presented. Here’s a link to the programme.  

 I presented two studies on my work from Skomer Island, home to probably the world’s largest Manx shearwater colony. 

My talk on Thursday morning showed how climatic variation in both the North and South Atlantic affects the survival and reproductive success of shearwaters, which migrate to the Patagonian Shelf. It’s a collaboration including Tim Guilford’s navigation group at Oxford and statistical wizards to make use of the Skomer’s long-term population monitoring data, initiated by Chris Perrins in the early 1970s (I took over in 2014). Several studies at the conference found that El Niño variation affects seabirds, from Europe to Australia to the sub-Antarctic, so we’ll be looking out for the effects of the current El Niño event that brought a heatwave to Cape Town early in the week.  

   
Then it was off to the poster session – in a few weeks I’ll be giving some tips to my dissertation students on how to do a great poster, so the pressure was on! Luckily I had a good hook, to grab the attention of the crowd. My poster was about a strange disease found in shearwater: puffinosis. Found only only in fledglings after they leave their burrows, the disease causes foot blisters and is usually fatal. My work used GIS analysis to try and explain the very predictable spatial distribution of the disease, which is informing the search for a cause. I’m part of another collaboration of ecologists, pathologists and geneticists looking into this, so watch this space! (I know what you’re thinking, and puffinosis isn’t found in puffins even though it sounds like it should be! The name comes from the scientific name for Manx shearwaters, Puffinus puffinus). 

 It was great to get some really useful feedback. I was quite tentative with some of my conclusions in my talk, and it was very encouraging to hear supportive comments and see that our results from shearwaters chimed with similar work in other species. Now it’s time to get the work published!

But you can do all this conference business online now, right? You don’t need to go all that way when you could just use new technology? Wrong! The most useful part for me was the amazing discussions after the presentations. I’ve made many new contacts with some really smart, helpful, and interesting people doing cool science – this will improve the quality of my science, and hopefully develop some great new work on seabirds. This morning I counted seven new potential collaborations – that would never have happened with a remote conference. A ‘real’ conference seriously helps to focus; your attention is fully devoted to it. The journey helps too, time to get ‘in the zone’ outward, and to reflect on the way home. 

And you can’t party online! Every conference has one, and it was unforgettable. The conference was introduced with a video message from Jane Goodall, who then gave us her rendition of a chimpanzee greeting call and challenged us to do the same for our study species. So last night, after a great conference week and a glass of wine or two, the world’s seabirders rose to Jane’s challenge! Here’s an impressive taster: three seabirders combining to mimic Leach’s Storm petrel. The rest will be online soon. 

I could write about the success of Twitter around the conference (check out #WSC2), the excellent venue and the scores of truly great talks and posters I saw, the impressive support for early career seabirders and the student protests about a 10% increase in tuition fees (I felt quite at home!), or how useful this trip has been for my teaching… but time and space are against me. 

I’m at Cape Town airport now, my plane’s about to board and my thoughts are turning homeward. This is the longest I’ve been away from home since I became a dad five years ago, and in this scintillating week my family have never been far from my mind. I’ll be home to see my wife and two boys very soon, and I’ve got some great stories to tell them. 

Sincere thanks to the University of Gloucestershire and JNCC for funding, and all the great people I’ve worked with to make these projects possible. 

Matt Wood

PS my five year old did his own poster about puffinosis this week. Clearly better than mine! And yes, that’s a bird-eating spider (centre right). He might be onto something…