Monday, 5 September 2016

The website for one of my new major research projects is now live!

TrypTag is a project to tag every gene in the trypanosome genome with a fluorescent marker to see where it goes in the cell.

Do you have no idea what I'm talking about? Read on to see what all that jargon means!

Trypanosomes are one of the parasites my research involves. They are single cell parasites that live in the blood, and they cause the diseases sleeping sickness in humans and nagana in livestock across Africa. All in all, not very nice.

Like all cells, trypanosomes are made up of protein machinery. Each protein is encoded by a gene in genome. A first step in finding a protein's function is finding where it goes in the cell. If you can map it to a particular structure then you have a good idea it's going to function there too.

To find where a protein goes in a cell we genetically modify the cell, sticking a fluorescent marker to the protein so we can see where it goes using a microscope. This is the process of tagging.

We are going to tag every protein gene in the genome, around 8000 genes, and build a complete map of the protein composition of the cell.

Tuesday, 16 February 2016

Looking at the structure inside cells

How complex and structured is the inside of a cell? It's hard to imagine, but the internal organisation of cells is typically precisely controlled by molecular skeletons and scaffolds, giving cells the shape they need to function.

We can discover the 3D organisation of the inside of cells using electron tomography; a process where you capture a series of images with an electron microscope, with the sample tilted at a slightly different angle for each image. This can then be used to calculate the 3D shape of the sample, using the same maths as for an X-ray CT scan.

Leishmania parasites are exquisitely structured. While they are only 2 micrometres wide (100 would fit across a human hair) they have a precise internal organisation which they faithfully replicate each time they divide. One of the distinctive parts of this organisation is the flagellar pocket, where the cell membrane folds in on itself at the base of the whip-like flagellum that the cell uses to swim.

In my latest paper, "Flagellar pocket restructuring through the Leishmania life cycle involves a discrete flagellum attachment zone", I used electron tomography to reconstruct the three-dimensional organisation of the Leishmania flagellar pocket. The structure in this area of the cell is incredible, and the journal picked a rendering of it for the cover image.

Volume covered in this 3D reconstruction is only 3 by 2 by 1 micrometres, about the size of a typical bacterial cell, but has enormous complexity. I have shown the microtubules (which make up most of the cytoskeleton) in red and membranes in blue. Each microtubule is only about 5 molecules wide, and is about 10,000 times narrower than a human hair! Some other specialised parts of the cytoskeleton are in green.

You can download the paper for free here to take a look at the structures in this area of the cell in more detail.

Software used:
IMod: Electron tomography structure
Blender: Tidying and rendering of the 3D structure