Tag Archives: in the lab

Adventures in protein land part 2: Cytosolic protein extraction

So this is going to be more like a lab book entry than anything else, but I’m finally starting to get my head around some of this protein malarkey and figured I should write it down in multiple places!  Continue reading

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Adventures in protein land

I’m not a protein biologist.

I wouldn’t usually describe myself as a geneticist either, unless trying to clarify what it is that I spend my time doing, in the same way that for years I would describe myself as playing the violin rather than as a violinist, because that seemed to indicate some level of skill that I didn’t feel I yet had.

But I’m definitely not a protein biologist, because I did no protein work as an undergrad, and I didn’t sign up to do a protein based PhD, and there’s only one post doc in the lab who has the first clue about proteins and – while she is possibly the most helpful post doc ever to cross my academic path – there’s only so much help someone can give you when you don’t know what questions to ask.

Yet in spite of this, I appear to be in a situation where doing protein work is inevitable. A few months ago I learned about PAGE gels and Coomassie blue staining and Western blots. Now, I must actually start extracting protein from real live plants, as opposed to my nice-n-easy-burst-like-a-bubble-E. coli. It turns out that this is rather more complicated than I had hoped.  Continue reading

The Ramen Diaries: Part 8 – Protein Extractions

After a week off with flu, there’s just no avoiding it. Today I have to get back in the lab and do my first ever protein extractions from a plant. I have a protocol, that I am assured works, and no reason to suspect it doesn’t. And I have been sat here for 54 minutes doing admin instead of even going to the greenhouse to get my plants. Looks like the stage fright is back. Le sigh….

The Ramen Diaries, Part 5: Where I throw a tantrum

When I was in my teens, the thing that I loved more about science was the opportunity to learn something new every day. I loved that what I thought I knew was never exactly true, and hated it at the same time. I wanted to know what we’d be told in our GCSE classes, or our A-level classes, or our undergraduate lectures long before I was old enough for it to be on the syllabus. I had this idea that if I kept studying science for long enough, eventually it would make sense.

It will never make sense.  Continue reading

Molecular Biology is like baking because…

If you are a sufficiently regular reader that you have ever googled me directly to get here, you will know that I am not the only baking biologist on the internet. In my haste and excitement to found my blog I neglected to realise that there is another baking biologist over on blogspot. Luckily, she mainly bakes, and I mainly biologise, so there isn’t too much cross over. Then there’s Sugar Scientist  and Domestic Diva MD and of course Dr Isis, Domestic Goddess.  It seems that baking is quite the past time for scientists in general and biologists in particular.

We have a running joke in the lab that there should be a list of questions that we ask to interview candidates before accepting them as members. It’s really a long list of things my PI dislikes about us (in a Grumpy Old Man way, rather than a genuinely-frustrated by way). The current list stipulates that new members of the lab:

– Must not have coloured hair (in the past 12 months alone mine has been purple, scarlet, royal blue and turquoise).
– Must not own cats
– Must not knit
– Must not have or use a mobile phone, especially in the lab
– Must be strongly opposed to the construction of pylons
– Must not read fiction
– Must attend the lab day out (my PI’s favourite day of the year is when none of us come in and he can have the lab completely to himself)

And the most recent addition to the list (thankfully, added after numerous successes not failures) is that new members of the lab must demonstrate their accomplishments as a baker. Because, ultimately, molecular biology and baking are very similar to one another in pretty much every respect other than scale.

Don’t believe me? Well let me explain…

A note from the lab bench

Dear internet,

It is infuriating to discover you have slipped up somewhere and ended up with next to no DNA or RNA or whatever at the end of your prep.

It is even more frustrating when you had planned really well and done everything to the letter.

But the most frustrating thing of all must be to be certain you have done it all right, have it all go wrong anyway and then discover someone else in the lab already knows why. 

I have (had? *sadface*) some RNA. I DNA-ase treated it prior to using it in qPCR. It needed cleaning up.

In the previous incarnation of this experiment I cleaned up the RNA (Qiagen RNA MinElute) then DNA-ase treated it. (Turbo DNAfree, in case you’re interested).

Except that the more I thought about it the more I worried that I was leaving residual DNase behind. So this time around I used the Turbo DNA-ase and then cleaned it up using an RNease Mini Kit. Exactly like it says you should. And all of my beautiful RNA is… well not gone. But coming out at ~50ng / uL. FIFTY. What the actual hell?! The other way around I got nearer TWO THOUSAND!!

Now obviously a MinElute elutes into 14 uL not 30, so it’s only natural to expect the prep to be half as concentrated: let’s say it was a pretty rough prep that would have had 800, then I might expect 400. But fifty?! Absolutely gutted and so unbelievably cross with myself for throwing all 14 samples at it at once.

But the most annoying part of all? Another PhD student in the lab figured this out about 2 months ago. Turbo DNA free and Qiagen RNeasy mini just aren’t compatible with one another and as far as I can see nobody has ever made a note of this.

Yours grumpily,

Baking Biologist