The Microbiome Votes: and the winner is…………

 

And the winner is Ed Miliband with his marvelous fungal quiff!

And the winner is Ed Miliband with his marvelous fungal quiff!

v3 v2 v1

The microbiome also likes the Green Party, perhaps not unsurprisingly!

The microbiome also likes the Green Party, perhaps not unsurprisingly!

Seems to have of the vote of my microbiome. Unfortunately, the bacteria have changed Nicola's features somewhat.

Seems to have of the vote of my microbiome. Unfortunately, the bacteria have changed Nicola’s features somewhat.

Ed

The toxicity of these three seems to have made the bacteria reluctant to colonise these individuals!

The toxicity of these three seems to have made the bacteria reluctant to colonise these individuals! Thanks for the suggestion Jo Milne.

My microbiome, that is the billions of bacteria that live on and in my body, in terms of cell number outweigh my own population of human cells 10 to 1. Given this numerical superiority, I felt it only fair that they get a say in deciding my vote in the upcoming general election. And so,  building upon a process first suggested by Poulomi Desai, I mixed my microbiome with the candidates and asked them to vote. Obviously, they are not able to tick a box, and so I “asked” the bacteria of my microbiome to move towards, and grow on the candidate of their choice. The results are just in!

On Light

Yes, that's me reading a newspaper using just the light Photobacterium phosphoreum HB.

Yes, that’s me reading a newspaper using just the light from Photobacterium phosphoreum HB.

Scaling up

Scaling up

An agar plate with  Photobacterium phosphoreum HB imaged by their own bioluminescence

An agar plate with Photobacterium phosphoreum HB imaged by their own bioluminescence

Single colonies of Photobacterium phosphoreum HB imaged by their own bioluminescence

Single colonies of Photobacterium phosphoreum HB imaged by their own bioluminescence

Single colonies of Photobacterium phosphoreum HB imaged by their own bioluminescence

Single colonies of Photobacterium phosphoreum HB imaged by their own bioluminescence

As a PhD student in the 1980s, part of my research project was to clone the genes that encoded the light producing machinery from naturally occurring bioluminescent bacteria, into more familiar bacteria like E.coli, and Staphylococcus aureus, where the light that these now produced as a consequence of my genetic interventions could be used to measure gene expression and viability. I would often spend hours in a darkroom, waiting for my eyes to become more sensitive in the dark, and then looking for the tell tale blue-green glow to tell me that my cloning experiments had worked. I’ve been beguiled by this unique biological light ever since, and have used it in my teaching to engage microbiology students. Quite often I’ve also taken this phenomenon outside the laboratory in order to share its wonder with the public. My latest bioluminescent adventure is with artist Anna Dumitru, and will be an installation based on the bioluminescent bacterium Photobacterium phosphoreum HB,  and will feature at the Wellcome Trust’s On Light event running from 1st to 4th May.

the letter m

M

I’ve been obsessing recently about the letter m.

Last week as part of our AHRC funded Metamorphoses project, Sarah Craske and myself took a copy of Ovid’s Metamorphoses from 1735, to the Surface Analysis Labs at the University of Surrey for analysis with Energy-Dispersive X-ray Spectroscopy.

In the lab, we carefully cut out a small sample of the book and placed into a aluminium sample holder ready for analysis. Now, I would have cut out a practical rectangular piece (I’m the scientist) but Sarah chose a more aesthetically pleasing circle (Sarah’s the artist), and we went ahead with this. We ended up then, with a small circle of nearly 300 year-old paper with the word “nondum” at its centre (again this was Sarah’s choice)

As preparation for its analysis, the paper had to be coated with a layer of elemental gold of just 0.7 nanometres in depth. For reference, gold leaf is typically around 0.1 micrometres in depth, and thus ~140-times thicker.

So we placed the ancient paper circle into the sputtering machine. At an appropriate state of vacuum, a swirling deep purple (maybe that’s where the got their name from) plasma flashed into existence, and danced briefly over our paper. When the paper was removed from the device, it had the faintest golden sheen to it, and I’m guessing that it had gained a little bit in value because of it diaphanous coating of gold.

For the analysis itself, our fragile and ancient paper disk was placed into a JSM-7100F Field Emission Scanning Electron Microscope (£500,000 worth of hardware) and its acceleration voltage ramped up to 5.0 kV.

The principal behind Energy-Dispersive X-ray spectroscopy (EDX) is that a high-energy beam of charged particles (electrons in our case) is focused into the sample of interest. The energy of the incident beam is such that it can eject an electron in an atom of the sample from the inner shell, creating an electron hole where the electron once was. Finally, an electron from an outer, higher-energy shell will then move in to fill this hole, and because it is more energetic than the hole that it now has to occupy, it releases this difference in energy as an X-ray. These X-rays are unique and indicative for each individual element, so that when they are measured, they reveal the identity of the element that they came from.

The machine then began to slam electrons into our ancient paper at speeds approaching that of light itself. Remarkably, as we watched the results of the high-energy electron collisions, and the collected X-rays from these accumulate on the computer screens before us, the letter m, the last letter of “nondum” began to form. Unlike our own eyes, which see the letter m because of the way that the ink interacts with light, the machine sees the letter for what it is really is, that is a small area and design made nearly 300 years ago from the element carbon.

Poised

Chemical systems carefully brought to the point of phase transition and then released from my control.