Teaching and Learning, OMIG 2014

I really dislike PCR. There. I said it.

OK, maybe I don’t really dislike PCR, but I don’t like when experiments don’t work. I find it hard to acknowledge the fact that doing a PhD is 10% intelligence and 90% persistence..life is very different in industry; if it doesn’t work, you leave it, or try one other thing to make it work.

Academic research is very different.. it brings to mind the phrase “if at first you don’t succeed, try, try and try again”. However, I had made a monumentally ridiculous transcription error (see what I did there!). Having had the PCR master mix recipe in my book (written by my PI for me), I had somehow managed to re-write this but during the copying over from one page to another, make a mistake in the volume of MgCl2 to add.. It went from 30uL to 5uL although I have no idea how I could have possibly done this..

Anyway, long story short, four failed PCR runs later, I decided to double check the master mix total volume..which didn’t add up, so decided then to check my PIs master mix and found the potential problem. the only other problem is that I have now spent hundreds of pounds on new reagents that I might not have even needed in the first place!!! My fingers and toes are crossed for tomorrow when Lucy kindly runs a gel for me to confirm amplification..picture to follow!

On a brighter note, I was accepted for a poster presentation for the OMIG meeting at Gregynog on the 12-14 March (tomorrow!!). So, five drafts of my poster later, and I picked up my final copy, perfectly printed (as far as I could tell after a quick glance) in A1 for presentation on Thursday (picture to follow too!). The hire car will be with me about 9am, leave mid-day and pick up Kirsty on the way through to Gregynog..looking forward to getting there and having the two course dinner 😀 (simple things 🙂 )

I finally met my first year undergrad MEDIC students this week too – in four groups, I gave a presentation of my PhD project in brief, and what the students are going to be doing as part of their practical project that I proposed a few months back. They all seem really excited to be doing it which is great, although not many of them knew much about microbiology, or candidosis..they will learn pretty quickly though I’m sure!

DM

Monday blues through to TGIF!

Monday morning came too quickly this week. Sat (what I hope to be) the last exam for he foreseeable future; Biomedical methods research techniques, and honestly..it was hard work! A lot about protein work, cell culture, bioinformatics but very little microbiology (one page of twelve total!) so not a particularly equal spread of questions over the course! Such a shame..but fingers crossed now until the results.

With the dreaded exam over, the rest of the week should really have been easy going – just get on with in vitro biofilm growth, confocal analysis on Wednesday, start again on Thurs and do adherence assays with more fluorescence analysis.. but no, this week had to be difficult!

Tuesday and wednesday came and went, the biofilms were analysed via confocal down at BioSci with Mark (who I hadn’t met previously..lovely guy, very helpful). Candida samples were great, worked well and got a few good images .. Streps however..grr! Managed somehow to get some kind of (what looks like Candida) contamination!, and there were some issues with the acrylic too, so couldn’t really get particularly great confocal images. On a good point though, biofilm thickness was about 25 microns again which is what I had hoped for (consistent with previous results, and some papers I have found since) :).

Thursday..what a pain, Cardiff Uni (dental school) have something called TESS..its a seminar series with invited speakers and internal speakers. now it hasn’t been running for quite some time, but this week was a visiting speaker looking at something completely outside of my research area, and of no real academic interest whatsoever to me personally (for others, it was very close to their projects so for them it was perfect!). But this seminar was compulsory for PhD students…compulsory! right in the middle of the day..when I should have been preparing to inoculate my acrylic..so that was scrapped for continuation today. Then today I realised that I said I would take Yuri to the confocal lab for his samples..so again, I couldn’t do an awful lot with my experiments! I did manage to get quite a few words written for my first year substantial report, but still..so glad this week is over and can hit the ground running Monday morning! Cannot wait!!!

DM

Oh, on another side note, I had an abstract accepted for a poster presentation at Gregynog in March 🙂 (didn’t get the oral presentation, but a poster is good none the less!!) So excited to give my FIRST poster presentation in this PhD, really looking forward to it 😀

Maths is not my strong point

Today, after being here at Cardiff University for about three and a half months doing my PhD project..working with bacteria, enumerating etc which if I’m honest is not the easiest thing to do in your head quickly, and using log values and the such..

Today is not like any other day, today I received my calculator. Woo! Now, this may not seem like such a big deal, but boy does it make me happy!

And what’s the first thing you do when you get a new calculator…calculate of course! Had to be done 🙂

2014-01-23 11.15.01

 

DM

Catching up!

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

Tattoo picture: 'If I have seen further, it is by standing on the shoulders of giants"
‘If I have seen further, it is by standing on the shoulders of giants”

DM

First week complete!

So my first week as a PhD student is complete – inductions complete, h&s stuff sorted, introductions to my academic colleagues done and settling in well.

Everybody is incredibly supportive; Rachael the amazing post-doc mum-like person, Kirsty my student buddy, Ray, Fraser, Niels, Lucy, Steve and fellow first year PhD student Paul!

Its like gaining a new family and an absolute pleasure to be a part of :). In at the mid-end next week (not quite the deep end..) with some PCR work on samples I sub cultured in my first week, ordered primers with Melanie which should arrive soon so that will be nice to do. Training day on Monday, and every monday for the foreseeable future!! Then just a lot more reading to do to try and get up to speed with the area. Fun!

Heres a picture of my new home 🙂

Cardiff uni desk
New home

Getting stuck in (kinda)

So, my first week as a PhD student has started. Generally quite organised – inductions were good and informative, and actually not boring! Lots of reading to be done, and just learning my way around is the biggest challenge at the moment!

Everybody is really friendly – the guys in the office are great..very supportive indeed!

Going to get stuck in tomorrow with my second supervisor..working with Candida isolates – subculturing just to get my feet wet, and then more literature reading and background searching! Its not boring yet..but that has the potential for change too!!

Nearly there

So, had a great meeting with my PI on Friday. Discussed ethics information for submission to the uni, contacts and provided some signatures, so its all systems go!

Now I have my university login details, time to start reading, reviewing, noting and learning about my project area..which means obtaining and spending some important time reading journals, papers etc. You know what it’s like if you have ever completed a dissertation project, or any kind of research essay! Cumbersome, mentally exhausting but so important, its not worth not doing!

Back to it! I’ll let you know how it goes 😀 just four weeks to go ’til I ‘start’!

And so it begins…

Hi, and welcome to my blog 🙂

I am an R&D Scientist; but not for much longer. In October of this year I embark on a PhD studentship at Cardiff University – School of Dentistry to undertake a research PhD investigating biofilms in denture stomatitis. It is a very exciting chapter in my life, and one that will inevitably make me an all round better person; personally and professionally.

It goes without saying that this next few years is going to be the most difficult of my life so far, but already feels as though it is going to be the most exciting (apart from the birth of my son or my wedding day..of course!). I am very much looking forward to the new challenges that lie ahead and with the support of my family know that it will be a huge success.

This blog is really just an ongoing diary of my studentship and goings-on in my life, so come and join me in my journey 🙂

Daniel