By Dom McGann
The summer’s sun cast a
gentle light over the trees as I approached the building that would be my
workplace for the next two weeks. Seeing the large wooden door and limestone
pillars of the Hopkins Building, I felt daunted by the realisation that I was
to spend a fortnight working in one of the most famous universities in the
I had been offered the
opportunity to work on a collaborative investigation between the Cambridge
Departments of Biochemistry and Zoology. The technical aspects of the study are
facilitated by Illumina, a world leading company in genetic sequencing
The aim of the project
was explained to me by Dr Welch during my first briefing at the Department. This
took place in a wood panelled library, lined with dusty volumes from the
infancy of biochemistry.
The investigation, set
up more than 15 years ago, was focused around beetles, in particular
Nicrophorus Vespilloides, a type of Burying Beetle. All Burying Beetles share a
common behaviour. When a female Burying Beetle has been fertilized by a male,
the pair locates a mouse carcass in which the female lays her eggs. The mouse
is then shorn of its’ fur by the beetles.
The pair then cover the corpse in a secretion, and bury it. It was noted that this secretion appears to
inhibit the decomposing power of the bacteria in the soil. The study strives to
find out why.
A deceased specimen of N.vespilloides
Dr Welch explained that
antibiotic medicines, such as penicillin, are derived from chemicals secreted
by bacteria or fungi in order to kill off other competing microorganisms. It is
believed that the beetles digestive tract, or exudate secretion, is host to
certain types of bacteria that secrete antibiotic chemicals.
My job was to identify
and isolate the 16S ribosomal RNA gene from N.vespilloides gut and exudate
extract. The 16S gene is a gene specific to bacteria; it is not present in any
other life form. It is an extremely large gene that controls protein production
within the organism, and is the reason why antibiotics don’t work on humans or
other large animals.
computer model of the 16S ribosomal RNA gene
Working alongside my
work placement partner Henry, I had to identify and amplify the 16S gene from
samples prepared for us by the Zoology team. We used a process called a Polymerase
Chain Reaction, or PCR. PCR is the most
important part of modern biochemistry. Discovered by Dr Kary Mullis, it allows
small amounts of DNA to be replicated , or amplified, in a very short space of
I found this process is
surprisingly easy, despite working with volumes of liquid smaller than a
1/100000 of a litre. However, I found the identification process rather more
PCR amplicons are
identified by a process known as gel electrophoresis. Armed with the pipette (the biochemist’s
weapon of choice) I had to inject 10 microlitres of my amplicons into tiny,
nearly invisible chambers in the gel. It took some practice to get right!
Nevertheless, the results were very rewarding.
The four pipettes with which I formed a strong bond during the week
My first successful gel in the electrophoresis chamber
For the gel to yield
the best results the DNA has to ‘run’ – or be allowed to settle through it - for
about 40 minutes. This period of waiting, usually occupied by tea and biscuits,
ends when the gel is removed, and observed under ultraviolet light.
When a gel is examined
under ultraviolet light the DNA bands glow. This is caused by a chemical called
ethidium bromide, which binds to DNA molecules causing them to fluoresce.
After the 16S gene had
been identified, I was left with the task of cutting the bands out of the gel
and re-extracting the amplicons from them for sequencing.
The sequencing for this
project was undertaken by Illumina, using a machine called the Mi-Seq, a
creation of my supervisor Dr Geoff Smith. I travelled to their facility in the
Chesterford Research Park for the final phase of my investigations. My samples had been transported there on dry
ice, in a secure vehicle, the previous day.
The ‘Mi-seq’, the smallest of Illumina’s machines, on
which our samples were sequenced
Above is a graphic
showing how the Mi-Seq works. Genes are broken down and reformed into vertical
strings, base by base, until the code can be read. By doing this with millions
of strings, the machine can fill any misread bases, and ensure accuracy.
The data from our
samples was sent off to analysts in America, who have the challenge of looking
for minute differences in the 16S gene.
This will give away the identity of its host, providing another clue to
the mysterious antibiotic properties of the beetles’ secretion.
I left the sparkling 21st
century halls of Illumina, a stark contrast to the wood panelled laboratory of
Cambridge, thinking of the destiny of my research.
I would like to think
that someday, the work of a teenager from a small town in Essex would assist,
even in the smallest way, with an advancement in medical science. Like the
beetles, I too could be a small part of a big discovery. It was with this
thought that I let the glass doors slide shut behind me, and walked into the
summer’s evening sun.