One necessary evil of doing a PhD is the thesis. Some see it as a celebration of the culmination of years of hard work, in a single volume of easy reading. It might well be, but it is still a very daunting task – 80,000 (give or take) words, flowing story, novel research communicated in a succinct, but scientific, and valid but not boring manner. Simple right!?
There is no best time to start – only “if you haven’t started yet, its already too late!”. That said, I have, if only for my own sanity, started writing, and while knowing my field somewhat better than I did two and a bit years ago, still struggle with the imposter syndrome that appears to rear its ugly head at the most inappropriate times. Do I really have the knowledge to write a thesis?! Am I going to have enough to make my three year journey seem worthwhile and sufficient for a doctoral degree?! Time will tell, and PIs of course..
Yesterday afternoon I attended a seminar all about social media, and my use of it as a researcher. We heard some really great talks; Joe Nicholls talked about why it is so important to have a social media presence for current a future research careers. Lucy Collins then told us about Altmetrics, and how social media usage impact can be measured (very interesting!), which is as important as journal impact factors for publications!
Having heard some inspiring talks, and all about the other side of social media (when it goes wrong..), I decided that my social media presence was a good thing, and plan to continue this. As a result, I updated a few things on the web (about.me for one) and invested in a domain to tie things together: danielmorse.me.uk 🙂
Next is to keep up to date and interact more with experts in my field (which I do already – mainly on twitter) and decide how to best separate (if necessary) personal/professional social media..tough one that!
You need a holiday, and then Easter holiday arrives, and your planned holiday to Burnham with the family does too! Fun times!!
The kids had a great time away, Oliver crawling like theres no tomorrow, Ruben winning another Minion toy not he grabber machine…on the last attempt! Time spent on the beach, in the arcade, in the pool (and on the slide!) and Ruben swimming like a pro. A well needed break away, and although I had a stinking cold for a few days through it, was good fun and lovely time spent with the family.
Back to work and getting things in motion for a busy few weeks of experiments. Host cell responses and biofilm interactions to do, sequencing data is starting to come back now so will have many meetings on analysing that no doubt – and let the supercomputer do the number crunching! So after a slow few weeks since Gregynog (with breaks and such), letting cells go, and grow again from LN stocks, things are looking ever more promising.
Had a lovely catch up with Chris from genesis (my old work) last week too – nice to see he’s doing well, and such a shame that he’s now left the company..but all good things..
I’ve also entered the Cardiff Half Marathon again this year, and am running for Stroke Association – hopefully we can raise some much needed funds to help those suffering with stroke (or helping those that suffer from them!). You can donate by visiting my just giving page (http://www.justgiving.com/danieljamesmorse) or by texting DJMO86 <amount> to 70070 (e.g. DJMO86 £5 to 70070) – I’d be really grateful if you could support me 🙂
So the plan for the past few days was to keep my cells growing (enough to use them soon if they grow quick enough!), do a bit of monocyte work and set up and maintain biofilms.. and it has once again proved to be a somewhat challenging but rewarding week at that.
Cells have established themselves very well indeed, and I’ve managed to grow enough to have two sets of freezer stocks, and two flasks actively growing, and the keratinocytes are doing pretty well too 🙂 (albeit significantly slower growing than the fibs!). Monocyte work didn’t really go to plan..as ever..but still, learning how, and having the confidence to use the flow cytometer on my own is somewhat an achievement as far as I’m concerned – a mere microbiologist using some fancy tech haha! Still haven’t got the result I was hoping for, but it seems as though it is getting close to being statistically significant in it’s own right..so watch this space!
Back to the biofilm work that I’ve missed for some time while developing my ‘skills’ in tissue culture.. I fixed some for later (CLSM) and took some for RNA extraction, using the same method, but pooled three biofilms together..and managed to get more than 10x as much RNA yield!! Purity is amazing..but yield is just incredible. Considering for the past 2 years I’ve been getting yields of 40-80 ng/ul, to get 500 as the lowest is a pretty good achievement!! Fingers crossed for the next lot of batches too! I’ll have more DNA than I know what to do with 😀 (at least now I can do some proper qPCR optimising too..primer checks and all that jazz with consistent samples of DNA). Super chuffed to say the least!
Next week is the last before preparations for OMIG begin (9th-11th March, Gregynog (so excited)), and I have medic students with me Monday pm and Wed (am), Thursday and Friday all day..should be fun (I think!). Anyway, today is Thursday which means Friday tomorrow, and I’m looking forward to spending a lovely day with my two boys at the museum, Ruben is really looking forward to seeing the dinosaurs, and Oliver will be too I’m sure if he knew what was going on! Fun times ahead 😀
It didn’t feel particularly busy, because working with cells means a lot of waiting for them to…well, grow. It’s all the little bits that seem to add up and make what seems like it should be an average week, into a very not average week.
Did some flow work at the start of the week which showed the new antibody I bought in worked :D. I also had another clinical sample – a stomatitis one this time too, so excited to see what comes back off the plates for isolated bugs..and need to sort the DNA extraction for that too.. good times! Nearly half way with these samples now.
My supervisor had his reviewers comments and scores for a grant application which he needed to get on with, and has taken such a long time to get this far (fingers crossed David!), so this week was mainly focussed on establishing cell lines after the infections, making sure my bugs were viable and growing ok, trying to ship cells from Sheffield and preparing abstracts and presentations! The cells did finally arrive this week after a nightmare with the shipping, but they’re now established and growing (hopefully well!). I managed to get images of all the tissues from the batch that were infected, which took forever to do…the bloody microscope is not very easy to work with, and the x40 mag sense is awful!! Does not work at all..
Wednesday was a good day…gave a presentation at the School of Dentistry Research Day – all about biofilms and my work. Went pretty well, had some good questions (which I think I answered ok!), and some great feedback from people after the talk which is always nice to get. Also submitted an abstract for Biofilms7 in Porto, Portugal – a biofilms related conference (it’s in the name!) so fingers crossed for the tone..next I’ll be applying for some money to actually go haha! Priorities 🙂
Next week is going to be a busy one..as it’s half term too, so staggered days of doing things, but should work out quite well I’m sure!
Time to go and pick up the kids now though!
This week was filled with anticipation; ELISA kits due to arrive, antibodies due to arrive, tissue models ready to be used for infections.. However, it quickly became apparent that this week was going to be a tough one!
After chaining the medium of the tissue models (all 36 of them..) on Monday, all was well. Until Wednesday. During the medium change on Wednesday, I noticed the medium was cloudy, and upon a quick look under the microscope I found the wells packed with what look like fungal spores, or yeast cells (Candida?)! Such a shame as these had been growing so well for about 3 weeks, and only now, two days before they were needed, they were infected. I collected some and took them for pathological analysis anyway to check the structure, and this is where the good bits come into play – the structure seems pretty good for a first attempt at tissues (and with cells that are known to be poor at tissue models!). H&E staining was great, and the thickness looks pretty good, just need to wait for a proper pathologist to take a look and critique!
Another high point was the arrival of the ELISA kit which now works properly! Thursday was a great day for this – the protocol finished, and showed a brilliant set of results – nearly exactly what I wanted to see – LPS influences pro-inflammatory cytokine release of monocyte cells :D. More work to be done..but watch this space!
And.. after 2 1/2 years here, I had my first fire alarm experience…and then another today! Two in two days, but nothing for the whole time I was here before. Thankfully no fire or damage phew, and all is well!
Busy week ahead with more monocyte priming/challenge work to be done, flow work, ELISA, qPCR and biofilms!! Busy busy 🙂
Whats happened since?
– I attended OMIG at Gregynog, which was my first conference. I presented a poster and won the poster prize! #Win
– I completed the MEDIC SSC project with grate success
– I attended the MITReG Conference in Cardiff and won second prize for my poster
– I passed my first year progress monitoring with no problems 😀
– A paper on which I was second author was published int he journal Biofouling. It encompasses my first years work and having spent an amazing year working with Yuri Cavalcanti, we managed to get this done.
– I went to Boston, MA, USA for the IADR conference and was accepted for an oral presentation
– I had another son – Oliver!
– I passed my second year progress monitoring with no problems
– I attended 3 conferences in 3 weeks; BSODR, Cardiff (oral presentation;) CITER, Bristol (oral) awarded Highly Commended; and GSK symposium in Weybridge (oral).
– I co-founded the Early Stage Researcher Peer Support Group (ESRPSG) with Kirsty which is going well
– I helped organise a conference (PGR Day) and was tasked with organising the external speaker (Robin Ince – what a guy!!)
– I spent 3 weeks in Sheffield University with Craig Murdoch and his group (Lucie, Luke) learning tissue model growth, which I’ve just started back in Cardiff too 🙂
Theres probably a lot more that I’ve just forgotten…but thats enough for now!
2016 has started slowly..with lots of things taking forever to get established, and things not working, but onwards and upwards so they say!
Wow, over three months since my last post..sorry about that!
So what have I been up to in the past three months?
– I’ve gotten stuck in with lab work; making acrylic pieces, doing adherence assays and growing biofilms on them (and looking at them using fluorescence confocal microscopy to determine depth and arrangement!). Also have done DNA extraction, run PCRs and purified samples (ready for sequencing) of my stock cultures.. all good fun but very important work for when my clinical samples start coming in!..
– Talking of clinical samples, IRAS (ethics) forms have been submitted and we are ready for the panel meeting which is going to be the start of Feb.
– Literature reading..and lots of it!
– Cardiff University have a yearly review for each PhD student, but instead of being at the end of the year (as it is called an End of Year Progress Report), its requested at 8 months!! This is a substantial report (9,000 words), including a significant literature review and details of my methods, results and conclusions to date.. all the hard lab work will be put on trial!
Since my last post, we’ve had Christmas and New Year – so happy new year to everyone that I haven’t yet seen/spoken to :). Christmas was lovely – spent a lot of time with the family which was great, Ruben had a blast with all his presents and it was really nice to be able to spend as much time with him as I was able to!
They say doing a PhD is 90% perseverance, 10% intelligence..and that is most definitely the case!! The trouble with growing biofilms, which grow for 7/14 days or more, is that if you get a single contaminant..that’s it! I found out the hard way.. one week in, I noticed that the media was changing colour by the end of each day and wondered why that was but just thought it was significant growth..no.. turns out I had contamination and all sorts grew when I enumerated my experiment! Three weeks worth of work (as I staggered the experiments) down the drain..just before Christmas!!! These experiments start up again this week, so fingers toes and everything that will physically cross are crossed in hope that this works (and I’ve stepped up my aseptic technique to avoid any issues 🙂 ).
One of my goals when starting the PhD was to do demonstrating/teaching at the undergraduate level. Well, my luck is in! I’ve managed to take part in a first year undergraduate medical students demonstrating scheme. I get a collection of 12 undergrads, and get them to do some practical work with me which is part of their curriculum (and it gives me teaching experience too!). I’ve chosen an adherence assay with some variables that are of interest to me, so they may even contribute toward my work progress in some way. I have to give them a presentation in March sometime, then they join me in May for a morning (in three groups of four students). Then they go away and analyse the results, and prepare a presentation of their work. They do a lot of the work, but I’m there to help point them in the right direction..should be good fun!
I think that’s enough rambling for now..I now have a reminder to post more frequently! 🙂
Ooh, and I got my first tattoo today!! #TattooTimes
‘If I have seen further, it is by standing on the shoulders of giants”