IAPETUS – Doctoral Training Partnership

I’m lucky and I know it. I’m lucky because my PhD studies are funded by the Natural Environment Research Council (NERC) through one of their Doctoral Training Partnerships or DTP’s (in my case IAPETUS – www.iapetus.ac.uk). Being part of the IAPETUS DTP has many advantages.

First and foremost is the supported feeling provided by being part of a cohort. In each funding year IAPETUS supports around 15 PhD students and these have all become firm friends. My IAPETUS cohort is split over the five partner institutions – Durham University, Newcastle University, St Andrews University, Glasgow University and Stirling University – and all studying in a range of scientific disciplines from oceanography to geology to glaciology to ecology and archaeology. The great positive of being brought together from such a wide range of backgrounds is that it is almost hard to talk in detail about our specific projects together, something that is often covered by laboratory colleagues. Instead we talk about the generalities of being a PhD student – of the struggle with samples, of frustrations with departments and maintaining a balance with regular life outside the PhD. Above all this creates a reassuring feeling of not being alone. Because of IAPETUS, I realise that no matter what discipline a PhD student is working in we all go through similar trials, frustrations and successes.

The second great advantage of being part of IAPETUS is the training opportunities it provides. From an induction day during November to a week at the Scottish Centre for Ecology and the Natural Environment (SCENE – http://www.gla.ac.uk/researchinstitutes/bahcm/researchfacilities/scene/about/) in cold January, training opportunities are plenty. These events have so far provided training in mathematical modelling, GIS, field sampling, experimental design, paper writing and presentation skills.

 

 

Additionally, it is a NERC requirement that we have a student conference/meeting once a year and this year we held the annual event in Majorca, Spain. This event was great and allowed for the best scientific poster session I have ever attended – see the photo if you don’t believe me! For the main part of our conference we were very kindly hosted by IMEDEA (Mediterranean Institute for Advanced Studies) and it was great to hear about some of the environmental research being conducted locally.

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From a personal PhD point of view, being on Majorca allowed me to visit Dr Joan Moranta at the Oceanographic Centre for the Balearic Islands to discuss barracuda sampling. I am very grateful to his support for my project.

In summary I am lucky and I know it. I am lucky to be part of IAPETUS and I would encourage anyone thinking of applying for a PhD to aim for becoming part of a DTP – you won’t regret it!

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An opportunity for learning…

One of the great things about studying for a PhD is the opportunities it presents for meeting new people, being exposed to new ideas and learning new things. Sometimes this arises in a more formal setting such as during seminar, conference presentation or training workshop but equally as often it occurs by chance meetings or discussions over coffee.  It’s often said that most real science is conducted in the pub!

Over the past few weeks I have had many of these opportunities. On the 15th of March, I and a few of my lab colleagues travelled to Cambridge University for the Evolutionary Genetics and Genomics Symposium (EGGS). This symposium was sponsored by the Genetics Society and provides an opportunity for researchers to share ideas and present their work. As a group we had decided that we would travel to the symposium and back in a single day – which made for a very early start and a late finish!

The symposium program had 15 talks scheduled through the day. The talks covered a range of topics from the evolution of viral resistance in rabbits (‘The rabbit strikes back: myxomatosis and the evolution of viral resistance’ – Joel Alves, University of Cambridge) to understanding the development of genitalia in Drosophila (‘Genetic and developmental basis of male genitalia evolution in Drosophila’ – Maria Daniela Santos Nunes, Oxford Brookes University). Sometimes it is easy to look at a conference/symposium program and all too readily dismiss talks as ‘not relevant’ or ‘unrelated’ to your own research. Sometimes this is indeed the case, but no matter what the topic of the talk there is something you can learn – from presentation skills, slide composition to even how not to do something!

Overall the day was a success, we heard some great talks, had chance to see some of the beautiful college buildings of Cambridge University and met some lovely people. We also looked around the fascinating collections of the Sedgewick Museum of Earth Sciences, a truly great institution – if you get a chance to go then really do! Thanks to the Genetics Society for sponsoring the symposium.

 

On the 21st of March I attended a three day Population Genomics workshop at Sheffield University. The workshop was funded by NERC and run by staff of the NERC Biomolecular Analysis Facility (NBAF) at Sheffield. Focusing on a variety of programs, the series of online tutorials and lectures during the workshop took us through a pipeline of bioinformatic data analysis. We could easily have spent weeks working through the problems provided but crucially the workshop provided an overview or taster of different methods and analyses. The knowledge and expertise of the workshop staff were incredible and I would recommend anybody with an interest to check out the services/opportunities provided at NBAF – http://nbaf.nerc.ac.uk/

In addition to these events I have also attended guest lectures both in my department and in my college at Durham. These can be especially varied. Early last month I attended two extremely dichotomous lectures on the same day, one on the effects of light pollution on wildlife and one on making medieval nautical charts! I love these opportunities for learning and it is one of my favourite aspects of my PhD so far. However, we mustn’t forget just how much I have learned from my colleagues. From lunch time chats to laboratory meetings I have probably learnt most from them, to the point I would say I couldn’t do my PhD without the support and knowledge of all the people around me on a day to day basis. A strong research group/team is invaluable and that is a lesson that I will remember forever.

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Social learning with the University College Sunday Seminar series.

Sequencing

The past few weeks have been very busy. I was due to be running my first sample set on the sequencer in January but due to a last minute drop out by another grad student I was bumped up to be on the end of November/start of December run. Running the Illumina HiSeq (the sequencer) is an expensive undertaking so in order to make it economical we fill the 8 sequencing lanes with samples from 8 different researchers, thus spreading the cost across projects. The trouble is that if somebody drops out then a replacement must be found quickly because otherwise the run is delayed and everybody suffers. So, with only four days notice I began to prepare my DNA libraries.

In order to sequence Restriction site Associated DNA (RAD) tags from many individuals at the same time and in the same lane we need to make sure that the sequence read from each sample is individually identifiable during the later analyses. To do this we follow the protocol of Peterson et al (2012) 1, adapted by Dr Kim Andrews (Hawai’i Institute of Marine Biology, University of Hawai’i). For me this involved taking 72 samples post enzyme digestion, ligating one of 12 unique barcodes to every sample in 6 groups. Samples from different locations were randomised across the 6 groups. Then the samples in each group were pooled before one of 6 unique indices were added to each pool; thus giving two levels of identification and allowing us to pull out individual samples after all 6 groups were pooled to make the final library.

This sounds simple enough but there are quite a few more quality control and quantification steps involved and when trying to do this in a rush it can be difficult. This whole process can be completed in 3 days if all goes perfectly. It would be advised to take longer however. In any case, I had problems with pool 5 and pool 6 and despite 12 and 13 hour stints in the lab to try and recover these pools we eventually had to drop pool 5 altogether. However, we managed to get out completed library to the sequencing facility in time (just!) and we have just had our preliminary data back. My PhD Christmas present is 233 million reads of DNA. That should keep me busy in the new year!

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The Illumina HiSeq next-gen sequencer at DBS Genomics

 

  1. Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S. & Hoekstra, H. E. Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLoS ONE 7, e37135 (2012).