Characterisation of coagulase-negative staphylococci associated with endocarditis

Coagulase-negative staphylococci are major aetiological agents of prosthetic valve endocarditis and an occasional cause of native valve disease. It is currently unclear how this group of usually avirulent microorganisms produces an infection associated with high rates of morbidity and mortality. The aim of this thesis was to investigate whether there are specific genotypes and/or phenotypes of coagulase-negative staphylococci with a propensity to cause infective endocarditis and to investigate any identified virulence factors as markers of infection. In this study, strains of endocarditis-related coagulase-negative staphylococci were genotyped by determining their macrorestriction genomic profile using pulsed-field gel electrophoresis. The strains were also investigated for phenotypic characteristics that predisposed the microorganisms to infect heart valves. By comparing coagulase-negative staphylococcal strains recovered from endocarditis patients with isolates from other significant infections (prosthetic device-related osteomyelitis and catheter-associated sepsis), no specific genotype or phenotype with a predilection to cause endocarditis was identified. However, the majority of the endocarditis-associated and other infection strains expressed the potential virulence factors lipase and esterase. Another approach to the investigation of virulence determinants used patient's serum to screen a Staphylococcus epidermidis NCTC 11047 genomic DNA library for cellular and secreted staphylococcal products that were expressed in vivo. The characterisation of two clones, which reacted with serum collected from a S. epidermidis-related endocarditis patient identified a staphylococcal pyruvate dehydrogenase complex E2 subunit and a novel secreted protein with homology to a Staphylococcus aureus staphyloxanthin biosynthesis protein and a secreted protein of unknown function described in Staphylococcus carnosus. Investigation of the secreted protein previously undetected in S. epidermidis, termed staphylococcal secretory antigen (SsaA), identified a potential marker of S. epidermidis-related endocarditis.

Real-time detection of DNA interactions with long-period fiber-grating-based biosensor

Using an optical biosensor based on a dual-peak long-period fiber grating, we have demonstrated the detection of interactions between biomolecules in real time. Silanization of the grating surface was successfully realized for the covalent immobilization of probe DNA, which was subsequently hybridized with the complementary target DNA sequence. It is interesting to note that the DNA biosensor was reusable after being stripped off the hybridized target DNA from the grating surface, demonstrating a function of multiple usability.

A technique to randomise consecutive codons in a sequence of DNA using MAX oligonucleotides

Randomisation of DNA using conventional methodology requires an excess of genes to be cloned, since with randomised codons NNN or NNG/T 64 genes or 32 genes must be cloned to encode 20 amino acids respectively. Thus, as the number of randomised codons increases, the number of genes required to encode a full set of proteins increases exponentially. Various methods have been developed that address the problems associated with excess of genes that occurs due to the degeneracy of the genetic code. These range from chemical methodologies to biological methods. These all involve the replacement, insertion or deletion of codon(s) rather than individual nucleotides. The biological methods are however limited to random insertion/deletion or replacement. Recent work by Hughes et al., (2003) has randomised three binding residues of a zinc finger gene. The drawback with this is the fact that consecutive codons cannot undergo saturation mutagenesis. This thesis describes the development of a method of saturation mutagenesis that can be used to randomise any number of consecutive codons in a DNA strand. The method makes use of “MAX” oligonucleotides coding for each of the 20 amino acids that are ligated to a conserved sequence of DNA using T4 DNA ligase. The “MAX” oligonucleotides were synthesised in such a way, with an MlyI restriction site, that restriction of the oligonucleotides occurred after the three nucleotides coding for the amino acids. This use of the MlyI site and the restrict, purify, ligate and amplify method allows the insertion of “MAX” codons at any position in the DNA. This methodology reduces the number of clones that are required to produce a representative library and has been demonstrated to be effective to 7 amino acid positions.

Real-time detection of DNA interactions with long-period fiber-grating-based biosensor

Using an optical biosensor based on a dual-peak long-period fiber grating, we have demonstrated the detection of interactions between biomolecules in real time. Silanization of the grating surface was successfully realized for the covalent immobilization of probe DNA, which was subsequently hybridized with the complementary target DNA sequence. It is interesting to note that the DNA biosensor was reusable after being stripped off the hybridized target DNA from the grating surface, demonstrating a function of multiple usability. © 2007 Optical Society of America.