17th June 2016 – Day 20

Friday: 
Two volunteers down today and there was a lot more western blotting to get done. Normal protocol applied and more antibodies were used, we re-probed all 5 blots and we photographed each of the 5 different blot membranes, none of them revealed anything apart from my second blot, which impressively showed a little something… woop woop!!


A very straight forward day, with lots of blots to come, which was nice but I cannot believe another week gone and that also means I am half way through my internship already!!

16th June 2016 – Day 19

Thursday:
I feel like I have written hundreds of these blog entries now and at this point you would think I would be bored doing the same things every day but when things don’t work, which it turns out yesterday's western blot was not successful, then we get to try again making small changes as we go. 
I completed all 6 pull down assays from Monday again but this time with a lot more amylose beads, hopefully something will stick this time meaning that the western blot might actually work.
All of the samples were prepared for the four gels which we will use tomorrow, I look forward to seeing if it will work. (Cross your fingers for me.)
While preparing each sample with the help of one of my colleagues, she somehow managed to spill half a millilitre of SDS loading dye onto the bench top (if only you could have seen her face, first shock and then a naughty smile), at which point she decided to try and clean it up by pipetting it with a 10ul tip (instead of wiping it up), the two of us trying very hard not to laugh, but the tip made little dent in the little purple ‘puddle’.
The samples that the volunteers prepared from yesterday’s pull down assay were run on 3 gels and transferred to a membrane, normal WB protocol was carried out. All of the membranes were stripped of their antibodies using stripping buffer (clever name!!) and left in blocking buffer overnight. We are going to probe these tomorrow with different antibodies.

Today was a little confusing but we got there in the end.

15th June 2016 – Day 18

Wednesday:
Already half way through the week and it still only feels like its Tuesday. I arrived at the lab this morning only to hear that the blots hadn’t transferred, this is so frustrating but I guess it is the nature of the game. After looking at them we decided that the SDS-PAGE gel might have been left in the transfer buffer too long, the protein appeared to have diffused out of the gel and therefore we chose to abandoned these blots and not take them any further.
Luckily we don't throw away our samples until we are one hundred percent sure we no longer need them and funny enough we forgot to put them into the fridge so they were still floating about… literally floating on what used to be ice. I fished out all of the tubes and re-did the two gels from yesterday, without the beads this time. (The one for staining and the other for the western blot).
I cracked on with this while the other three volunteers carried on with pull downs assays using nickel beads and three different protein samples, from samples that were previously harvested.
It was a slow paced day but between us, we achieved a lot. The other three finished the pull downs and got them ready to transfer to a gel, which will be done tomorrow.
Everyone else left but I stayed on, I wanted to carry on with other things during the hour long incubation steps. I made all of the buffers that I would need. I do enjoy making blocking buffer (who would have ever thought about using milk powder in a western blot, genius!). I made some more de-stain for the gels, I got so excited when I was told I could do this, more clean fresh de-stain. It’s so transparent, no dye in it yet...... I suppose it’s like the bio-bins all over again..... can't help myself.
I started on with the western blot on my own and finished at 6 pm as anticipated, and really proud of myself. I carried out a western blot from start to finish all on my own, no mistakes, and finished when we had planned. So a good day all in all…. Well except for when I dropped the transfer buffer upside down into the tub upon where it all emptied out and almost went everywhere ...... but excluding that then. 
During incubation time of the antibodies on the membrane, I had a chance to take some photographs of all of the other gels, of which there are many.  It is easy to get them confused, but I was careful to ensure to label the boxes as we go.
Once the western blot was completed, we took a photograph of it, sadly it didn’t show much in the elute fraction with the amylose beads. It was very disappointing to see, well technically not to see, but we definitely know it worked because the histag antibody attached to the marker which has showed nice and clearly.
I’m really pleased to be home filling in my practical notes and just preparing mentally for tomorrow, I will be doing another western blot…cross fingers this one actually shows us something of use.

During the morning catch up with Amy while we were discussing what we were going to be doing for the day, I saw out of the corner of my eye, someone sneak into the lab and nick one of our new bio-bins, I realise now that perhaps we shouldn't have flaunted our wealth quite so much. Haha but at least we know where the new stash is being kept.

14th June 2016 – Day 17

Tuesday:
We continued the pull down assay with the proteins and bead that I put on to incubate overnight. We loaded the flow through samples on to one gel and the beads on to the other two gels.
The stained flow through gel appeared to have a lot less protein than before…. which is good it means that more proteins have bound to the beads this time.
The other 2 gels with the elution and bead samples were transferred to a nitrocellulose membrane for western blotting.


While the gel was running we prepared 2 more SDS-Page gels. Once transferred, the membrane was put in blocking overnight.
We then decided to optimise the beads used for the pull down and used a mixture of amylose beads for one protein and nickel beads on an identical protein in order to compare them. We ran all of the samples on a gel.
 

Today was very challenging-phew!!

Day 16 – Shadowing James

We were in the cell culture room, special lab coats were needed (there were only larges left)



13th June 2016 – Day 16

Monday:
Three extra pairs of hands from volunteers filling up the lab today and what a huge difference it made, making light work of the protocol.  If that wasn’t lucky enoughwe received some new bio-bins!!! The excitement on my face when one of my colleagues told me, I laughed and asked what the occasion was, it felt like Christmas.......why she found this so funny I don’t know, all I know is that I am easily pleased and happy to have some new bins. 
In the briefing with Amy this morning we discovered that over the weekend the first protein was applied to the GF column, the fractions were collected and loaded onto a gel. Amy also purified Sufu, but she didn’t run in on a gel before applying it to the column. Both protein fractions were pooled and concentrated.
Once we had been brought up to speed on the weekends work, we set off making gels… always the first thing we do at the start of a week. 
2 setting SDS-PAGE gels
 
Following that we started a pull down assay using amylose beads, purified Sufu, MBP (our control) and our 2 proteins. We are investigating whether Sufu interacts with our other proteins. We used the amylose buffers we made on Friday and collected the Flow through, the wash and the elute. This is a very similar method to purification using beads, the only difference being initially you add 2 proteins to the beads instead of one.

Each collected sample was prepared with loading dye and run on 3 gels. Once they were running, we made 4 more gels for tomorrows SDS-PAGE. With all of the additional help from the volunteers, we managed to get through everything really quickly. As a result I had some free time while the gel was running and I went down to one of the larger labs and had a chance to shadow James, a PhD student, who is working with human leukaemia cells.  It was amazing to see the culturing process which is slightly different to working with bacteria.  I was shown how things are kept sterile using ethanol, how things are disposed of and I learnt some new techniques which I hope to put to good use soon. Observing this PhD in progress using human cell lines and a new technique has cemented my career decision and passion to pursue my own PhD!! It was nice being in a different environment and being able to enjoy the nice cool air-conditioning (whilst Amy told stories of my excitement at getting new bio-bins causing much laughter).


We got the results from the gel and discovered that not much protein bound to the beads therefore next time we will prepare fresh samples of beads with the proteins and add more binding buffer as well as incubate for a longer period overnight with rotation in the fridge. 

I had such a good day today, I really enjoyed it, it was exciting to learn something new..... role on tomorrow!

10th June 2016 – Day 15

Friday:
I received an email from Amy saying that there isn’t much to do today and that I could have the day off – yay for a long weekend!  However Amy spent the day continuing the experiment from yesterday, which was basically repeating this week's protocol after the initial incubation temperature of colonies were changed… so all in… straight forward. Amy concentrated the second protein elute further, she applied in the GF column, same as before, 9 fractions were taken and run on a gel (so also all rather straight forward)








The Sufu that we had harvested and frozen yesterday was re-suspended in lysis buffer, sonicated and was purified the same as before, leaving it to be incubated overnight at 4˚C. (Amy says she wants to come in over the weekend to finish it off, after which she will also apply to the GF column.)

9th June 2016 – Day 14

Thursday:
Today we took the fractions from the GF column and ran them on a gel.
I love this picture, the bands are so clear, there is no contamination between lanes, this is what an SDS-PAGE gel should like… the way each of the proteins have separated by size… I am pleased with how this has come out.
Once we had decided which fraction from the GF column contained our purified proteins, we pooled the fractions (concentrated, quantitated, aliquoted and flash frozen).

Concentrating columns
The new cultures we made of Sufu and the second protein we harvested (same as before), were frozen, thawed and then the second protein was re-suspended in lysis buffer. The protein was purified the same as before and we collected all of the samples and ran them on a gel… I’ve done this so many times now that I am almost an expert.
The elute sample of the second protein was concentrated and stored overnight.
Once that was all finished we prepared the two buffers which we will need for the pull-down assays next week.
500ml of Amylose Binding buffer
200ml of Amylose Elution buffer
These were nice and straight forward buffers to make, very similar to the purification buffers we made last Friday.

It was a very challenging day, but we got there in the end!!

8th June 2016 – Day 13

Wednesday:
29˚C in the lab today, we had everything open, windows, doors, everything and it was still too hot. The university was having some form of a sports day and we could hear all the cheering coming in through the windows. We all kept getting a fright as the horn sounded throughout the day, creating a nice atmosphere and keeping us on our toes despite the heat of the day.  (We all looked for an excuse to go down to the phd labs, or the room at the back where we get our ice from, the rooms with the air conditioning .... just so we could cool down a bit.) 
Today we finished off the third protein purification, taking the same samples as we went along to run on a gel. 

We concentrated the third eluted protein the same way we did the Sufu and it was applied to the GF column.

We really knew what we were doing today as we have done it so many times this week, this made things a little more straight forward which was a good thing because of the heat.

7th June 2016 – Day 12

Tuesday:
We analysed the Sufu fractions from the filtration column on a gel. We then pooled the fractions from the GF column (concentrated and quantitated, aliquoted and flash frozen).
The column was washed with water and ethanol and we had to change the size of the column for the second protein which is much smaller in size.
The Gel Filtration Column
The Histag purification was completed with the second protein and samples were taken at each stage and run on a gel.
Looking at the gels, most of the proteins for both were found to be insoluble and we decided to do instead of do can you say run the cultures again but this time incubate them at 18˚C instead of 37˚C overnight. So we began again, making fresh cultures for all and a new broth for the giant culture flasks. We decided to go ahead with the purification of the third protein which we did and incubated overnight again with rotation.

I keep thinking its Thursday, we have done so much in the last 2 days that I feel like it should be the end of the week. I guess the heat doesn’t help, the labs have been incredibly hot (the weather report lied, they said it would rain, it never did, we need just a little rain to cool us down).