All entries for June 2007

June 29, 2007

Briefing 2

Hi all,

Nice to see you all today. Hope you found the session useful and enjoyed your lunch!
I’ve uploaded some photos to the Briefings gallery (those labelled Briefing 2 are from today…) for the benefit of those of you who were unable to attend.
Hope your projects go well and don’t forget to keep us updated on how you’re all getting on!


June 26, 2007

URSS – everyone seems to have finished and i've only just started!

Okay this is my first attempt at a blog, i still havent really figured it out.
I’m just on my lunchbreak for my second day of placement in the Warwick Biological Sciences department, up on Gibbet Hill. I am working with Dr. Kevin Purdy and my project involves looking at the distribution of methanogens (methane producing bacteria) in the guts of different termites.

I havent seen any termite guts yet however (thankgod!). Kevin has focused on teaching me the techniques involved with the amplification of small amounts of DNA, PCR, and also the technique of running that DNA on an argose gel to guage its length. My first PCR was a success, sucessfully amplifying the 1500bp sequence the primers coded for. I have got a photo, a little bit sad i know but i was really happy that it actually worked as i have heard so much about how frustrating sciece can be when things don’t work, will post the photo soon if i can work out how!

Really enjoying my time here, there is alot of waiting around for reactions to happen so i can see how frustrating it must be if things don’t go to plan but luckily mine have so far, i am sure i will a post a slightly stroppier frustrated blog when things do go wrong though!

For now a happy microbiologist!

June 23, 2007

NMR Week 2

Had a good second week (or second three days due to the Final Fling)! Ran another two guanosine spectra and felt a lot more confident with the use of the 300MHz spectrometer. One of our samples gave an abnormal spectrum initially, but after weighing it and noting that there was more of it than the previous samples the problem was proposed to be due to too much signal being given out. After decreasing the spectrometer gain and rerunning it, a better spectrum was obtained.

I practised using the Simpson simulation program for a good few hours by making notes on all of the parameters and then running and adapting example simulations to test whether I really knew what everything meant.

A comparison of two of the samples:
Spectral comparison of two samples (updated 05/07/07)

June 13, 2007

NMR: The first week

Day 1

The aim of my project is to use NMR to determine the structure of six synthetic guanosine-based compounds. My supervisor and the PhD student I’ll be working with gave me an outline of the tasks I will be doing..

So far I have helped to pack one of the samples into a Bruker 4mm rotor which is then placed into a probe which fits into a 300MHz spectrometer.

Using the spectrometer requires a lot of setup, for example the probe has to be tuned and the system and settings calibrated (by comparing the spectra of an alanine sample to one made previously). After going through it all, Amy and I set the sample to run overnight, using the NMR pulse sequence known as Cross Polarisation. I hadn’t come across this sequence before so it’s likely that there’ll be a fair bit of reading involved before I can be confident that I understand the procedures!

Day 2

We got results! The spectra was compared to the known spectra of guanosine so the extra peaks were identified as being those corresponding to the additional parts of the molecule. I learnt a bit about Double Quantum Coherence: a phenomenon which will be of great use in determining which atoms are adjacent to which in a molecule and their separation distances.

The second guanosine based sample was set to run overnight. I had a bigger part to play in the spectrometer set-up this time, which was quite a test of my 24 hour memory!

Day 3

Learnt more about Double Quantum Coherence and the pulse sequence that is used to exploit it. We set histidine (another amino acid) spinning in the spectrometer and saw results which matched known information.

Also managed to prepare a plan! A lot of it presumes we can get spectrometer time though.

Day 4

Drew lots of molecules using various software…was really fun! And they look so cool! Scoured databases to find molecules similar to the ones we are working on. When one was found we downloaded the structure and tried to see if the software used would allow us to add molecules in it to make our specimens. From there it will be possible to run computer simulations on it in order to obtain spectra without actually doing one experimentally.

Day 5

Observed and assisted with the use of the 600MHz spectrometer and then read the instruction manual to try and remember key points about its use. I find it really hard to remember things I’m told so making notes and rereading manuals is a must for me! Started learning how to use the simulation program too.

June 2007

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