Interleukin 6 (IL6) is associated with arterial disease development, progression and surgical outcome. Raised levels of IL6 may play a causal role in disease development or may be the effect of pathology. An IL6 single nucleotide polymorphism (SNP) G- 174C has been identified and reported to associate with IL6 expression. However, conflicting results have emerged and both the relationship between IL6 and vascular disease and the precise effect of SNP G-174C in vivo in humans remains obscure. The aim of this study was to establish the effect of SNP G-174C in humans, in vivo in different tissues. Varicose vein surgery patients donated adipose tissue, skeletal muscle, vein and blood samples. Patients were genotyped for SNP G-174C. A new pre-mRNA assay was developed, using gel electrophoresis, restriction digest and fluorescence quantification, to measure the ratio of heterozygous allelic pre-mRNA transcription. IL6 mRNA expression in different tissues was also measured using relative real time PCR (RT-PCR) to assess effect of tissue type on expression profiles. mRNA expression within tissues was compared between G-174C genotypes, to further quantifying the association of SNP G-174C with transcript levels. The pre-mRNA assay showed higher expression for the C-allele, though not statistically significant. The pre-mRNA assay needed to detect low levels of intron retaining allelic pre-mRNA isoforms. Replicates and controls for residual genomic DNA were used to monitor assay precision. Adipose tissue gave the greatest precision in the pre-mRNA assay. In the RT PCR assay adipose tissue expressed significantly more IL6 mRNA than all other tissues examined. In vein and leukocytes subjects with the CC genotype expressed significantly higher levels of IL6 mRNA than subjects with GC or GG genotypes. There was a trend towards higher expression for the CC genotype in all tissue types. A significant though weak correlation between IL6 mRNA expression and age was demonstrated for vein and leukocytes. Adipose tissue may be an important source of IL6 compared to other tissues. This may be relevant for obesity associated diseases. Subjects with G-174C genotype CC showed a trend towards higher IL6 RNA expression. Further studies are necessary to clarify the effect of genotype on IL6 expression.

DNA sequencing has vastly opened up the world of molecular biology, leading to new areas of interest, especially in medical research. Unfortunately the methods of DNA sequencing have only ever seen gradual improvements, as Sanger sequencing is still very much the norm despite its high cost and slow speed. Nanopores present an exciting opportunity for DNA sequencing, however, despite the concept being presented in 1996 several problems have prevented the creation of a publicly available sequencing device. The two main focuses of research into nanopores so far have been improving the resolution between bases and the slowing down of DNA translocation through the pore so modern ammeters can read the sequence accurately. The simulation work presented in this thesis largely focuses on the energetics associated with DNA translocation. This is performed in several parts; an investigation into the probability of pore entry, study into the free energy of translocation for two proteins in addition to solvent contribution to this free energy, finally a theoretical project was undertaken to investigate bottom up nanopore design.

Hi-Spot are highly re-aggregated neural cultures grown on PTFE membrane at the liquidair interface. The Hi-Spot protocol was developed by scientists at Capsant Neurotechnologies using embryonic neural tissue. We characterised Hi-Spots made using existing protocols to confirm they represented a maturing neural network with molecular, cellular and functional signatures. We have additionally modified existing protocols to allow use of postnatal tissue as the source for dissociation and re-aggregation. Hi-Spots made from postnatal day zero (P0) rats self organised into a complex 3D tissue-like structure containing anatomically synaptically-interconnected neurons, astroglia and microglia. This CNS analogue of brain tissue provides for the emergence of a co-ordinated excitatory and inhibitory network, demonstrating a maturing pattern of activity involving single spikes developing into bursting behaviour driven by intrinsic synaptic activity. This activity can be represented as frequency or averaged amplitude (RMS), increases with time in culture and is blocked by glutamate receptor antagonists and stimulated by the inhibitory receptor antagonist bicuculline. The validity of its more in vivo-like organization, not observed in more conventional dissociated cultures, is evidenced by a glutamate toxicity resistance in the Hi-Spot cultures. Further, the thesis describes the optimisations to the Hi-Spot protocol to allow viable high density re-aggregated cultures to be made from individual rather than pooled brain dissociations. Modifications to the protocol included dissociation of the mouse tissue using a protease papain kit and cell plating at an increased cell density. Using this as a platform we have gone on to investigate the neuronal dysfunction occurring in Cysteine String Protein (CSP)α-/- mice. CSPα is a presynaptic protein thought to have co-chaperone like functions, mice lacking CSPα are born alive but show progressive weakness and neuronal degeneration soon after birth (Fernandez-Chacon, Wolfel et al. 2004). Hi-Spots formed from CSPα -/- tissue did not show overt neurodegenerative characteristics compared to +/+ controls and functional analysis demonstrated that at~DIV14 CSPα +/+ and -/- mice displayed equal levels of basal spontaneous network activity. Addition of bicuculline (50μM) to +/+ cultures lead to a significantly increasedfrequency and RMS value. However, in -/- cultures there was no increase induced by bicuculline. This may be due to an inability of CSPα -/- cultures to sustain high frequency synaptic transmission that is associated with bursting activity, or a selective degeneration of a sub-population of inhibitory neurons and a homeostatic network plasticity. The data suggest CSPα may act to protect the ability of neurons for high frequency synaptic transmission and/ or protect inhibitory neurons from degeneration.

No description available.

Our ever increasing knowledge of genetics is radically changing disciplines in science and medicine. Significantly, the study of gene expression and protein synthesis within both healthy and abnormal cells has advanced understanding of the mechanism of disease at the molecular level. The future treatment of certain diseases may benefit from new classes of nucleic acid based drugs which are currently undergoing development and trialling. Concurrently, assays are being formulated to predict, diagnose and monitor medical conditions. This more detailed patient analysis brings the option of moving away from traditional, textbook treatments and tailoring therapies to the individual, the field of personalised medicine. Current polynucleotide analysis platforms allow testing for genomic mutations and quantification of gene expression on a massively multiplexed scale with some arrays able to identify more than a million unique target sequences in a single assay. However much development is required to take this analysis technology from laboratory based applications to the bedside. Reductions in assay costs and analysis time are particular concerns. The 4G research group, based at the University of Southampton has developed novel encoded microparticle technology, allowing individual particles to be identified in a mixture. The work herein documents the adaption of this technology for the multiplexed analysis of DNA samples in the form of a suspension/hybridisation assay, a design which may offer advantages over current analysis technologies including reduced assay time and increased array flexibility.

Click chemistry has the potential to be employed for the assembly of large DNA fragments, by purely chemical methods. However to enable this, the bio-compatibility of the resulting click-linked DNA must be examined. Click DNA linkers were incorporated into a plasmid within the gene encoding for an ampicillin resistance marker. The plasmid was transformed into E. coli and resulting colonies found to survive on LB agar plates supplemented with ampicillin. This indicated that the click DNA linker was replicated and transcribed correctly by the cellular machinery of E. coli. The observed bio-compatibility was further probed by demonstrating the functionality of the click-linked DNA in nucleotide excision repair deficient cells line. The bio-compatibility of the click DNA linker was then investigated in a non-essential gene by constructing a click-linked variant of the gene encoding for the fluorescent mCherry protein. Experiments carried out using a plasmid containing two click DNA linkers in the region of the gene encoding for the mCherry fluorophore provided further evidence that the click DNA linker was functional in E. coli. Moreover, using a coupled in vitro transcription/translation system the yield and fluorescence of the mCherry protein expressed from the plasmid containing the click DNA linker was similar to that from canonical DNA. Investigation of the bio-compatibility of the click DNA linker in mammalian cells showed that a plasmid containing the click-linked DNA, had the same viability of a plasmid containing canonical DNA. Finally, the use of click ligation for the assembly of the first 229 bp of the mCherry gene was investigated. Two different approaches referred as “templated click assembly” and “one-pot click assembly” were employed and the bio-compatibility of the click DNA linker was confirmed in both cases.

No description available.

Predictive Adaptive Responses are changes in development made in the perinatal period in response to maternally transmitted information, and a mismatch between the diet selected during human evolution and the contemporary Western diet can produce an adult phenotype characterised by weight gain, cardiovascular disease, hypertension and diabetes. In humans, most evidence is epidemiological. Using Drosophila melanogaster, the problem can be approached from an adaptive phenotypic plasticity perspective. Health effects in humans stem from predictive adaptations made to enhance fitness and so it must first be shown that D. melanogaster make these responses. To model the human dietary transition, two equivalent fly diets were designed, one a human Palaeolithic diet and the other a contemporary Western diet. Using isofemale lines, flies were swapped between diets over three generations and fitness indicators measured in the offspring generation. Fitness indicator responses to a range of diets differing in protein: carbohydrate ratio and total macronutrient content were also investigated. There were adaptive, compensatory effects on survival rate and male thorax size from parental diet, and development time from grandparental diets, but also non-adaptive effects on development time and female thorax size from the parental diets. Higher dietary protein: carbohydrate ratios reduced development time and increased thorax size and survival rate, while increased macronutrient content increased weight, lipid content and survival. Diet had no effect on ommatidia number relative to fly size. Whether a response to diet is predictive and adaptive depends not only on diet composition, but whether offspring, parents or grandparents consumed the diet, the phenotypic character measured and the genotype of the fly. The variety of responses in relation to parental and grandparental diets show that intergenerational effects are complex, and D. melanogaster is a suitable model to help unravel the causes of human diseases.

DNA is regularly subjected to endogenous and exogenous reagents that cause mutations that can be detrimental to a cell if they are not repaired. One class of enzymes responsible for DNA repair is the family of DNA glycosylases and their role is to remove damaged bases. Uracil DNA Glycosylase (UDG) is a member of this family and is highly specific, removing only uracil, an RNA base, from DNA. Uracil arises in DNA through misincorporation of deoxyuridine monophosphate (dUMP) creating an A.U base pair, or through deamination of cytosine resulting in a G.U base pair. Though UDG acts on A.U pairs, this is not it’s primarily role as A.U pairings are not mutagenic. However the G.U mispair is highly mutagenic and leads to a G.C to A.T transition on subsequent rounds of replication. UDG only reacts with uracil and has no activity at thymine since the 5-methyl group on the base is excluded from the active site. This thesis examines mutants of UDG that can cleave cytosine but not 5-methylcytosine. Methylation of cytosine at CpG sites leads to gene silencing and is an important epigenetic signal. Knowing the methylation state of cytosines will therefore be important for understanding gene control and may be beneficial for treating many diseases. The most common method for detecting cytosine methylation uses a bisulphite reaction followed by normal DNA sequencing methods. This process has several drawbacks and the aim of this work is to create an enzyme that is capable of distinguishing between5-methylcytosine and cytosine. It has been reported that mutation of a critical asparagine in UDG to an aspartate allows the enzyme to accommodate cytosine into its active site; generating a cytosine DNA glycosylase (CDG). Using the natural ability of UDG to distinguish between uracil and thymine due to the presence of the 5-methyl group, we hypothesised that the mutant enzyme should be able to discriminate between5-methylcytosine and cytosine, which differ by the presence or absence of a methyl group in the same position. E. coli and human CDGs were prepared and their ability to remove cytosine or 5-methylcytosine examined when placed in different sequence contexts. hCDG was generated through complete gene synthesis of hUDG followed by the N204D mutation. The corresponding mutation in E.coli (N123D) generates a highly cytotoxic enzyme that cannot even be cloned in pUC19. As L191 aids base flipping, mutation to alanine (L191A) renders the enzyme inactive; activity can then be rescued using a bulky synthetic nucleoside that occupies the base pair and forces the target base into an extrahelical conformation. The L191A mutation was followed by N123D to generate an expressible and functional eCDG, denoted eCYDG. We demonstrate that these mutants have cytosine glycosylase activity when the cytosine is mispaired or unpaired, but not when paired with guanine, and show no activity against5-methylcytosine in any context. The activity of these CDGs varies with the stability of the base pair, with the fastest cleavage rates being obtained with the least stable base pairs, and also varies with the local sequence context. As CDGs are able to discriminate between cytosine and 5-methylcytosine we began development of a real-time PCR assay for detection of 5-methylcytosine. This employed a hexaethylene glycol (HEG) linker opposite the target cytosine, as this produces one of the fastest cleavage rates and cannot be read by a DNA polymerase.

Porphyrin moieties were rigidly attached to DNA to generate an accurate molecular ruler. Molecular ruler analysis was conducted using steady-state fluorescence, circular dichroism and small angle X-ray scattering spectroscopic techniques, in an attempt to analyse the FRET, exciton coupling and scattering intensity between different porphyrin-porphyrin labelled DNA combinations. A 21-mer test sequence was labelled with a porphyrin in one position on one strand, and seven different positions on seven complementary strands, to overall give seven porphyrin-porphyrin inter-strand combinations. Steady-state fluorescence and circular dichroism spectroscopic analysis of the Soret band revealed individual Watson-Crick bases pair molecular ruler sensitivity. Small angle X-ray scattering attempts between metallated-porphyrin entities did not reveal sufficient scattering at low concentrations, in contrast, an iodinated analogue of the porphyrin system did displayed scattering correlating to different iodine iodine distances. After calibration of the porphyrin system, the moieties were applied to study protein-DNA interactions between Tus, a 36 KDa DNA binding protein, and Ter, a specific 21-mer DNA sequence. Molecular ruler nalysis of the complex required an extended version of the Ter DNA sequence to which modifications were attached. Established FRET pairs FAM and TAMRA were applied to investigate protein-DNA complexation. Native PAGE analysis revealed Tus binds to the extended DNA via a sliding mechanism. Fluorescence analysis of the established FRET pairs identified changes in fluorescence not correlating to changes in FRET, and instead was attributed to emission quenching upon protein binding. Applying the zinc and free base porphyrin version displayed subtle changes in the Soret band circular dichrosim upon complexation, indicating small DNA helical change upon complexation. A 45-mer DNA sequence was designed to form multiple hairpin-duplex conformations with the addition of an appropriate complementary strand. Attaching FRET pairs to the extremes of the DNA sequence enabled multiple DNA conformations, and hence FRET distances to be obtained from one doubly modified DNA sequence. The combinations were characterised by UV-Vis, fluorescence and circular dichroism spectroscopy. Finally, terpyridine labelled DNA sequences selectively formed DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. Short DNA strands were designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as zinc induced the formation of tubular arrays consisting of DNA bundles 50-200 nm wide and 2-50 nm high. TEM displayed additional long distance ordering of the terpyridine-DNA complexes into fibers.