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

Ergodic Analysis

My review paper about ergodic analysis came out on Thursday. Does ergodic analysis sound terrifying? It's actually quite a simple concept and it is a powerful method for extracting information about the dynamics of a cell division cycle from a single snapshot of cells at random stages of the cell cycle.

Ergodic analysis is particularly useful if a time-lapse video is impossible, for example if the cells swim or you want to do an analysis that kills the cells.

Does this sound interesting for your research? Drop me a message: @Zephyris.

Software used:
Autodesk Sketchbook Pro: Drawing the cells.
Inkscape: Page layout.

Light-Years of DNA

Light-year, and DNA. Not two scientific terms you expect to see on the same page, but over your lifetime your body will produce around one light-year of DNA! That is about one trillion kilometres. Don't believe me? Let's do some maths:

Every cell in your body has two copies of your genome, held in 23 pairs of chromosomes. The human genome is approximately three billion (3×10⁹) base pairs of DNA.

The famous double helix of DNA has about 10 base pairs per twist, and each twist is 3.4 nanometers long (3.4×10^-9 metres, the same as roughly 20 carbon-carbon bonds).

This means that the total length of DNA contained in every cell of your body is approximately 2 meters (3×10⁹ base pairs multiplied by 0.34×10^-9 metres per base pair, doubled because of the two copies).

Your body has about ten trillion (1×10¹³) cells (excluding red blood cells), and this remains roughly constant through your life. There is a huge turnover of these cells though, as your body replaces cells to maintain itself.

Every time a cell is replaced its 2 metres of DNA must be produced. In most tissues the cells are replaced in a couple of months, and in many they are replaced in just a couple of days. Even cells in bones are replaced every few years.

The average lifetime of a cell is probably one or two months, so if you live to 80 then your cells are replaced about 500 times throughout the course of your life.

This means that the total length of DNA your body produces in your lifetime is approximately 1×10¹⁶ metres (2 metres multiplied by 1×10¹³ cells, multiplied by 500 replacements). 1×10¹⁶ metres (ten thousand trillion metres) is about one light-year (0.946×10¹⁶ metres)! Most amazingly it would not be a light-year of random DNA sequence, but ten thousand trillion identical copies of your DNA, faithfully replicated by your cells.

References:
An estimation of the number of cells in the human body
How quickly do different cells in the body replace themselves?
Thanks to Rob Phillips for making me think about this!

Tree of Plants

Everyone knows what plants are like; they have leaves and roots, flowers and seeds. Or do they? All of these classic features of plants are actually relatively recent developments in plant evolution. Conifers don't have flowers, ferns don't have seeds or flowers and moss doesn't have leaves, roots, seeds or flowers! Leaves, roots, flowers and seeds are all features that evolved as plants adapted, starting at something like seaweed, to life on the land.

This term's issue of Phenotype has a bit of a focus on plants, and my research comic for this issue focuses on how plants evolved and adapted to land. You can download a pdf of this feature here, the full issue for the summer (Trinity) term will be available soon here.

While I was making this I started reconsidering just what the plant life cycle looks like, as a classic school education about how plants reproduce isn't very accurate! The classic teaching is that the pollen produced by a flower is like sperm in mammals (and humans), and the ovum in the flower is like the egg in mammals. In fact pollen and the developing seed are more like small haploid multicellular organisms, gametophytes, that used to be free living. If you go back through evolutionary time towards ferns then the gametophyte is a truly independent multicellular organism. Go back further still and the bryophytes spend most of their time as the gametophyte.

If you imagine the same evolutionary history for humans then it is easy to see how different this life cycle is to animals; if the ancestors of humans had a life cycle similar to ferns then, roughly speaking, ovaries and testicles would be free-living organisms that sprout a full grown human once fertilisation successfully occurs. I can't help but think that would have been a little strange!

Software used:
Autodesk Sketchbook Pro: Drawing the cells.
Inkscape: Page layout.

Cheeky

Human cheek cells are a classic subject of school microscopy. It is easy to collect some by gently scraping the inside of your cheek. This is a high resolution phase contrast image of one of my cheek cells, put together using focus stacking of a 4 by 4 montage of 57 focus slices using one of my ImageJ macros. The detail of the nuclear structure, the granular contents of the cytoplasm and the structured surface of the cell really jump out.

This cell is quite large for mammalian cells, about 75 μm across, and around 10 times larger than the single cell Leishmania parasite I currently do much of my research on. If you have sharp eyesight you can even see human cheek cells by eye (although only just) when they are spread on a slide.

Like most mammalian cells, cheek cells are essentially transparent. If you use a microscope in the most basic way, essentially as a giant magnifying glass, shining light straight through the sample towards your eye, you see something like this:

Bright field micrograph of a human cheek cell.

This picture has even had the contrast artificially enhanced. Practically it is tough to even find the cells on the slide and get them in focus!

For many years the best alternative was oblique or dark field microscopy. Here you deliberately avoid shining light straight through the sample, and instead make sure that only light scattered by structures in the sample can collected by the objective lens and get up to your eye.

Dark field micrograph of a human cheek cell.

Images by dark field microscopy can be hard to interpret, and are typically limited to fairly low resolution.

More complex methods based on interference of light travelling through the sample were developed in the 20th Century. These methods, phase contrast and differential interference contrast, were a revolution. They allowed completely new approaches for looking at the biology of cells, particularly live cells and dynamic processes like cell division. They were such a revolution that the inventor of phase contrast microscopy, Frits Zernik, was awarded the Nobel prize in Physics in 1953 for this work.

Phase contrast micrograph of a human cheek cell.

DIC micrograph of a human cheek cell.

It was not until the development of the famous green fluorescence protein, for fluorescence microscopy in live cells in the 1990s, that there was another discovery which improved the capacity for live cell microscopy to the same extent as phase contrast and DIC.

Software used:
ImageJ

Mould

Have you ever looked closely at mould?

Look closer...

Classic pin mould, like you often find on decomposing fruit, is an amazing micro machine. The head of each pin contains the developing spores which are released to spread the mold. This release process ranges from the gentle to the extreme, from a gentle puff of spores to one of the fastest events in the natural world. The hat thrower fungus pin head fires off the end of the pins with an acceleration of 0 to 45 mph in less than 1 mm; an acceleration of over 20,000 g.

Software used:
UFRaw: Raw to tiff conversion of raw camera files.
ImageJ: Focus stacking.
Hugin: Panorama stiching.

The Shape of a Cell

Each term I make a research comic for the Oxford University Biochemical Society magazine called Phenotype. The topic for this cartoon; the function of cell shape in bacteria. You might not know, but bacteria can have one of a huge variety of different shapes, but why cells have a particular shape is not a commonly asked question. To quote Kevin Young: "To be brutally honest, few people care that bacteria have different shapes. Which is a shame, because the bacteria seem to care very much.".

Check out the comic here, the whole issue will be available to download for free from here soon.

Software used:
Autodesk Sketchbook Pro: Drawing the cells.
Inkscape: Page layout.

Building a Human

Every single cell in your body is made up of four main types of chemical compound: protein, carbohydrate, lipids/fats and nucleic acids. You are made of molecules, precisely defined and complex molecules, but still just molecules.

The difference in scale between a person and a molecule is enormous. A person is around one to two metres tall. A typical chemical bond is around one to two ångstroms. One ångstrom is tiny; one ten-billionth of a meter. If you took the entire population of the Earth, scaled each person to the size of a typical atomic bond and then stacked everyone head to toe, then the stack would be about your height. This means that, while you are made of molecules, it takes a lot of them to make a person!

The most common type of complex biological molecule in your body are proteins. These are the molecular machines that run your cells. Proteins are made up of chains of different combinations of 21 different amino acids. The amino acids themselves are quite simple molecules; typically made up of 5-10 carbon atoms, a couple of nitrogen and oxygen atoms and a sprinkling of hydrogen. We now know enough about protein amino acid sequences, the structure of cells and the structure of proteins that we could make a pretty good effort of making a scale model of a person, or at least the proteins that make them up.

This picture is a plastic scale model of 100 amino acids, representative of all the amino acids in your body, at about the ratio the different types are used to make up the proteins in your cells. They are ready to clip together to make a scale model of proteins, at a scale of about one centimetre for a bond (100 million times larger than the molecules they represent). Using enough copies of this (and lots of plastic models of water molecules) you could make an accurate scale model of 75% of your body. You would need a lot though; 1,000,000,000,000,000,000,000,000 copies of this set of 100 amino acids. The scale model of your body would also stand around 100,000 kilometres tall (1/3 of the way to the moon), and would weigh much more than the entire Earth.

Your body is an incredible molecular machine, made up of a near-unimaginable mixture of complex biological molecules, all running at a molecular scale. Next time you see someone talking about nanotechnology stop and think for a second. You are nanotechnology; a self-organising, self-repairing, reproducing, thinking piece of nanotech.

Software used:
Blender: 3D design of the plastic scale model.