As their biology it is thought that they

As
PICI elements are novel in terms of their biology it is thought that they can
serve as a novel antimicrobial therapy and utilised as a ‘Trojan Horse strategy
in vivo’. By exploiting the relationship between the conflicting phage and
bacterial genomes, we can begin to realise the potential of PICIs to hijack
integral proteins encoded by the phage to interfere with phage reproduction
strategies and genome packaging mechanisms. In doing so, the helper phage is able to efficiently
replicate, package and mobilise synthetic PICI elements only, which can; introduce
accessory virulence factors into a new host, provide the ability to supress
antibiotic resistance in different species of bacteria (thus making them
susceptible to antibiotics), or target biofilm formation in cannulas and
catheters etc. By engineering PICI elements in this way it is possible to
target specific strains of bacteria (even within the same species) without
disrupting the natural microbiome of other commensal symbionts present in
different niches (i.e. within the colon). As a result, PICIs can provide the
key to developing a novel antimicrobial treatment which can circumvent the complications
associated with traditional antimicrobial therapies in a strain specific manner
while potentially eliminating the need for broad spectrum antimicrobial
treatments which exacerbate the myriad of ill effects associated with AMR.

The
experimental aims involve exploring new and better medicines which can combat
bacterial infections using synthetic phage-inducible chromosomal islands
(PICIs). Using a dual science approach I will attempt to characterise different
PICI elements in different species of bacteria including Staphylococcus aureus, Enterococcus durans, Enterococcus faecalis and
Escherichia coli. Theoretically, by modifying the PICI DNA and proteins it
is possible to target different bacterial cells in a strain specific manner,
therefore this approach has great potential to see the emergence of a new antimicrobial
treatment with means to fight off bacterial related infections within clinical
and agricultural settings. Additionally, as this topic is relatively new and
unexplored, expanding upon the PICI family to include more species and gain a
deeper insight into the functionality of many genes which remain ‘unknown’ or
‘hypothetical’ is also an area which I am keen to address.

The work involved is primarily based on bacteriology
where experiments such as phage titration assays will be performed to determine the number of
phage particles in the original culture so that known amounts of virus can be
used to infect cells during subsequent experiments. Phage induction will be carried out to produce PICI
particles which can manipulate helper phage mechanisms to become mobilised,
thus enabling transfer of their own genetic material (i.e. antibiotic
resistance genes) at high frequencies, to susceptible bacteria via horizontal
gene transfer. Complementation
assays using plasmids will be employed to obtain information on the location of
gene mutations (if present on different genes).  It is also possible to use the complementation
assay to determine the relationship between the genotype and phenotype, i.e.
the molecular events which govern specific mutations, conferring characteristic
phenotypes observed in different diseases. In addition to other culture based
and culture independent methods used, computational analysis will be will be carried
out to create and check genomic mutations (i.e. base deletions) in bacterial
and phage DNA sequences while enabling the design of specific oligopeptide
primers for use in PCR. The design of microfluidic devices will
be applied to this study and serve as a valuable tool to obtain rapid turnover
of data in the form of colorimetric readouts.

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