Category Archives: Molecular Biology 101

Molecular Biology 101: Synteny, Conservation and two wheat genomes

Somehow between going to the Netherlands, the Easter break, a week-long lab course and a conference talk to write I managed to miss not just one, but two really interesting, exciting and useful papers in Nature (Incidentally, I try not to write too much on here related to my PhD: I’m always a little scared that I’ll end up saying similar things about papers in my literature review and then being pulled up for plagiarism or something, but these are two interesting to miss.) But I digress.

Sequencing the wheat A and D genomes

Two weeks ago a consortium of Chinese and American scientists published two papers about sequencing both the A and the D genome progenitors for bread wheat. (Quick re-cap for the un-initiated. Wheat is a hexaploid i.e. instead of having one maternal and one paternal copy of each chromosome – that is, 2 in total, it has 3 pairs of each, making its genotype AABBDD). This is pretty big news for a couple of reasons: Continue reading

Molecular Biology 101: DNA testing

Today, archaeologists from the University of Leicester announced that they believe they have found the lost grave of the last English King of the house of York, Richard III. They have been testing bones believed to be his to compare his DNA with that of known descendants in order to confirm his identity. This is a pretty similar process to the DNA testing we hear about all the time for paternity tests, or forensic studies: but how does it actually work? Continue reading

Molecular Biology 101: A map from here to there (and the barley genome)

Barley and Wheat are pretty similar. After all they’re sisters… No really. In a flash of food-security related brilliance I named my guinea pigs Wheat and Barley. Let it never be said that I don’t take my PhD seriously…

But seriously: wheat and barley are both cereals; important food crops, important feed crops, vital for producing my two favourite beverages (20% of the worldwide narley yield goes for malting), not to mention bread… Wheat tends to get a lot more coverage though: the world grows around a quarter of the amount of barley that it does of wheat and the amount spent on barley-related science is therefore always likely to be a bit lower.  Continue reading

Idiot’s guide to Western Blots: Part 1

Having not touched them since … June maybe? Perhaps even May … I’m back to doing Western Blots, a technique that I wasn’t amazingly confident with to begin with. I did a dry run with samples that didn’t matter on Friday, knowing that Iw as likely to make tonnes of little mistakes all over the show, forgetting things that once seemed too intuitive to write down. What I need, I thought to myself, is an Idiot’s Guide.

There’s something that bothers me about Idiots’ Guides: They never tell you where something will go wrong. Or what will happen if it does. So here I present the Baking Biologist’s guide to Western blotting: The things that can go wrong, why they will go wrong, and whether to carry on or just scrap the whole thing.

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Molecular Biology 101: qPCR when you need to detect duplication events

Why are you in work so late?! asked my housemate’s boyfriend, when I explained via Facebook chat that that was where I was.

I got really into writing. And now I’ve been here so long that the qPCR I planned to run over night is done, so I may as well do the analysis! I replied

Dedication to the cause! Came the reply. But I have no idea what qPCR is…

I pride myself on talking about science far too much and boring everyone around me, especially housemates and their boyfriends. So how have I possibly avoided explaining what qPCR is?!

DNA Replication

 DNA exists in relatively small quantities compared to how much we need to do molecular biology. In order to work with it – or, for that matter, check whether it is there – we need to make more of it. A particularly awesome feature of DNA makes this possible. It is a double stranded molecule: if you could straighten out the helix that it works itself into it would look like a ladder, and the two sides are inverse copies of one another. (Once you have finished marvelling open-mouthed at my non-existent artistic skills you will, I’m sure, spot that pink always pairs with orange etc).

This means that if you split the molecule in two, it’s possible to rebuild the other side from the side that you have. This happens inside your cells all the time and is called semi-conservative replication.

The Polymerase Chain Reaction

We can simulate this in the lab through a reaction called PCR (Polymerase Chain Reaction). PCR can best be summed up by my favourite geeky advert of all time. (A geeky advert so immense that for my first 4 months as a PhD student I drank from a BioRad mug for no other reason).

In case that was all a bit much for you, here’s a quick recap:

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Molecular Biology 101: What’s an -ome when it’s at home?

Genome

Proteome

Transcriptome

Exome

Microbiome?

All of these words are becoming part of the scientific vernacular, and new ones are arising all the time. But is this proliferation of terms meaninful, or even a good thing?  Continue reading

Molecular Biology 101: QTL mapping, and salt-tolerant chick peas

At the time of writing, the world population clock shows the total number of people on Earth as 7, 052, 499, 082. A smidge over 7 billion. And according to the FAO around 1 billion of those people are starving. The current prediction is that by 2050 the world population will have increased to around 9 billion people, and in order to feed all of those people we will need to produce at least 70% more food than we currently do. (We’re also eating more meat, which is more energetically expensive, because not all of the energy in a bowl of corn goes into the meat of the chicken who eats it, which is why it’s so much higher than 2/7.)

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