The ability to resolve the individual frequency components of a complex sound is known as frequency selectivity. The auditory system seems to act as a series of overlapping band-pass filters or auditory filters (AF), the width of which describe frequency selectivity. It is a fundamental and extensively studied property of the auditory system, yet its neural basis is not fully understood. This is due, in part, to the fact that two distinct approaches are taken to explore it; psychophysics and physiology, the results of which are difficult to reconcile. AF are measured in quite different ways in the two sub-fields. Psychophysics measures the ability of the system as a whole by using masking paradigms to measure the bandwidth of AF from behavioural data. A preferred method in human psychophysics is notched noise (NN) masking using forward masking with fixed signal level, since it does not suffer from confounds like suppression and off-frequency listening. In physiology bandwidth can be measured for single cells, or a population of cells, at various levels of the auditory system, and is traditionally done by observing the number of action potentials elicited in response to pure tone stimuli. The auditory system is known to be highly non-linear and so comparing the results of such vastly different approaches is problematic. Also, psychophysics measures the detection threshold of 'signal' sounds; how this compares to mean spike rates used in physiology is not clear. Attempts have been made in the past to apply the same method in animals to measure both psychophysical and physiological bandwidths, with varying degree of success. No successful attempt has been made to use an up-to-date method used in human psychophysics. In this thesis I take a step towards comparing psychophysical and physiological results by 1) developing a novel method that allows forward masked NN bandwidths to be measured behaviourally in the ferret, and 2) applying the same psychophysical paradigm to measuring bandwidth in guinea pig inferior colliculus (IC) and primary auditory cortex (A1) neurons. In addition a signal detection theory (SDT) approach is used on the physiological data to make results more comparable to psychophysical ones. Results from the behavioural method show that it can be used to successfully measure both forward and simultaneously masked NN bandwidths in the same animal, and that these measurements are in close agreement with one another and with bandwidths measured using previous methods. Results from the guinea pig physiology study show that bandwidths measured from IC neurons using the psychophysical NN paradigm are narrower than pure tone estimates of bandwidth, in the same neurons. However, the NN estimates are in close agreement with auditory peripheral and perceptual bandwidths, a finding which differs substantially from previous studies. Unexpectedly, however, bandwidths estimated from A1 neurons using masking show much finer tuning at high frequencies than seen further down the auditory system. This tuning is not only narrower than pure tone tuning in these neurons, but also finer than psychophysically measured estimates, which represent the auditory system as a whole. However, this may be related to the greater non-linearity of cortical neurons compared with those in the midbrain and lower. This work demonstrates that it is possible to reconcile different measurements of tuning in the auditory system by using appropriate methods. It also highlights the complex nature of auditory neurons and how care must be taken when measuring frequency selectivity using different approaches. In addition it provides a method for measuring auditory bandwidths psychophysically and physiologically in the same animal, allowing a direct comparison between the two; a vital step in investigating the neural basis of perceptual frequency selectivity.

Hypothalamic tanycytes are a specialised type of glial cell found lining the 3rd ventricle. They possess a cell body that contacts the cerebrospinal fluid (CSF) and a single long process that projects into the hypothalamic parenchyma, some of which are known to extend into the Arcuate nucleus (ARC) and Ventromedial nucleus (VMN), two key hypothalamic regions involved in control of energy homeostasis. Owing to their unique position, it has been hypothesised that hypothalamic tanycytes may be able to detect nutrient related signals in the CSF and influence the neurons of the ARC and VMN leading to changes in food intake and body weight. Tanycytes have recently been shown to be glucosensitive, responding to brief application of glucose by generating Ca2+ waves. However the signalling pathways inducing this response remain elusive. Here we investigated the nature of tanycyte glucosensing. Using Ca2+ imaging techniques we show that tanycytes can respond to glucose and non-nutritive sweeteners implicating the sweet taste receptor as the mediator of tanycyte glucosensitivity. We further show that activation of the sweet taste receptor induces release of ATP from tanycytes via pannexin hemichannels allowing propagation of the Ca2+wave. In addition we also investigated whether hypothalamic tanycytes can communicate to secondary cells within the hypothalamus. Using multiphoton stimulation of a single tanycyte, we show that Ca2+ waves can be generated, which spread between neighbouring cells as well as along the tanycyte process towards the hypothalamic parenchyma. We also demonstrate signalling in secondary cells following tanycyte stimulation is likely the result of tanycyte communication. Thus hypothalamic tanycytes are able to detect sweet tasting compounds in the CSF via the sweet taste receptor, this induces Ca2+ signalling which may be communicated to secondary cells, including the neurons of the ARC and VMN, where it may be integrated to induce changes in energy homeostasis.

Atherosclerosis is characterised by the deposition and accumulation of modified lipids in the subendothelial space of the arterial wall, as well as vascular remodelling leading to atherosclerotic plaque formation. Restenosis is a known complication of the surgical interventions used to treat atherosclerosis and results in neointimal thickening, in part by the action of vascular smooth muscle cells (VSMCs). Various physiological effects have previously been attributed to the action of oxidised low density lipoproteins leading to an exacerbation of the inflammatory response and vascular remodelling processes in atherosclerosis and restenosis. Little is known to date about the effects of individual modified lipids generated by the action of phagocytic myeloperoxidase (MPO) on these processes. The aim of the present study was to investigate the biological effects of modified lipids, both chlorinated and oxidised species, in vascular injury and disease, focussing primarily on their effects on vascular smooth muscle (VSM). Primary VSMCs were used to examine the effects of these modified lipids at a cellular level. Chlorinated lipids, phospholipid chlorohydrins and alpha-chloro fatty aldehydes were found to have a limited effect on VSMC proliferation, viability or migration whereas, oxidised phospholipids caused a concentration-dependent reduction in all of these vascular remodelling processes. As AMP-activated protein kinase (AMPK) has recently been implicated in vascular disease and found to exert anti-apoptotic effects, the impact of AMPK signalling on the effects of the modified lipids in VSM was assessed. Activation of AMPK prior to incubation of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine chlorohydrin resulted in an increase in VSMC proliferation while a greater level of VSMC death was observed after treatment with the oxidised phospholipid, 1-palmitoyl-2-oxovaleroyl-sn-glycero-3-phosphocholine than with the lipids alone. The occurrence of these modified lipids in neointima formation was subsequently investigated using a carotid artery injury model in healthy and atherosclerotic mice (mice deficient in apolipoprotein E, ApoE-/-). Neointimal growth and levels of plasma MPO were increased in ApoE-/- mice resulting in elevated levels of lysophosphatidylcholines and altered relative proportions of phosphatidylcholines (PCs) in injured carotid arteries compared to their contralateral uninjured right carotid arteries. Finally, in vivo AMPK activation by administration of 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) in healthy and atherosclerotic mice and its effect on the lipid profile of the aorta were characterised. Chronic AMPK activation resulted in a reduction in mean arterial and diastolic pressures as well as a dramatic increase in pulse pressure in ApoE-/- mice compared to their saline-treated littermates. Plasma MPO was elevated in AICAR-treated ApoE-/- mice with an alteration in the relative intensities of PCs in aortae of AMPK activated ApoE-/- mice. The present study is the first report of divergent effects of different classes of modified lipids on vascular remodelling processes and how these processes may be modulated by AMPK signalling in VSM in atherosclerosis. In addition, this study has generated novel data on the relative changes in distribution of PCs in carotid arteries after vascular injury as well as in aortic tissue of healthy and atherosclerotic mice after AMPK activation. Additional analysis is required to confirm these differences which could offer further insight into the involvement of modified lipids in vascular diseases. This study has also highlighted a novel interaction of AMPK signalling and modified lipids in VSM and could therefore provide novel therapeutic targets in the treatment of both atherosclerosis and restenosis.

The object of this work was to characterise the interaction between beef liver glutamate dehydrogenase (EC 1.4.1.3), the inner mitochondrial membrane and its constituent phospholipids. Because of the similarities in the structure and properties of detergents with phospholipids, interaction of the enzyme with both types of amphiphiles was investigated. Interaction with phospholipid membranes was found to be a reversible process while detergents brought about irreversible denaturation at high concentrations. Association between the enzyme and the amphiphiles showed that the nature of the head group determines the extent of complex formation. Zwitter-ionic lysolecithin and phosphatidy1choline showed no interaction, while the anionic sodium dodecyl sulphate, phosphatidylserine and cardiolipin showed high affinity for binding to the enzyme. The apparent Ki values in the case of the two phospholipids were found to be 1 - 2 u M and 3 - 5 uM respectively in the direction of reductive aminatlon, The possibility of different conformations of the enzyme binding specifically to these charged surfaces and conformational changes brought about as a result of complex formation was investigated. The extent of binding decreased with increasing pHand ionic strength, suggesting contributions from electrostatic interactions. Evidence for hydrophobic interaction was indicated by the observation that the extent of complex formation increases with increasing temperature. Binding of the enzyme to mitochondrial membranes also indicated similar types of specificities. The enzyme showed a much higher affinity for binding to the inner surface of the inner mitochondrial membrane than to the outer surfaces of the inner and outer membranes. The extent of binding was also shown to depend on the presence of metabolites such as NADH and ADP. Binding decreased with increasing pH and ionic strength as was found for pure phospholipids. It is suggested that, in mitochondria, the reversible association between the enzyme and the inner mitochondrial membrane is controlled in a manner dependent upon the local pH, ionic strength and metabolite concentrations, and this may have important physiological significance in the control of metabolic activities of the enzyme. It is also suggested that the system exhibits the allosteric phenomenon which may be important for its regulation.

The interactions of 4-aminopyridine with the delayed potassium conductance of skeletal muscle have been investigated. It is ! fo~nd that 4-aminopyridine (4-AP) is 10 times more potent than TEA ions in blocking the potassium conductance, and in addition 4-AP appears to block in a different way. (2) 4-AP is a weak base with a pKa of 9.17. The distribution of such a weak base across the cell membrane and means for determining which class of the base is responsible for the biological activity are discussed. (3) When 4-AP is present on both sides of the membrane, the peak potassium conductance is reduced and there is an initial faster component to the timecourse of inactivati.on. When 4-AP is present on the outside of the fibre only the peak conductance is reduced (Kdiss =l.lmH). (4) It is proposed that the cationic form of 4-AP is the active form and that it acts at two sites. One is accessible from the extracellular solution and is responsible for the reduction in peak current; and the other accessible from the intracellular solution and responsible for the initial faster component of inactivation. (5) After an initial delay the inactivation induced by 4-AP inside the fibre, 4-AP:, is found to d.ecay exponentially at a rate which ~ increases as the internal potential is made more positive. (iv) (6) The fraction of channels that become inactivated by 4-AP+. in the' 1 course of a depolarizing step is found to increase as the internal potential is made more positive. In the voltage range -4OmV to Omv this fraction undergoes an e-fold increase every l2mV; beyond +lOmV this fraction reaches a limit, the value of which depends only on the concentration of 4-AP. (7) The blocking actions of 4-AP outside the fibre, 4-AP + , can be o separated into two components. One component is not influenced by the membrane electric field and the level of block depends only on the concentration of 4-AP. The second component is influenced by the membrane electric field and undergoes an e-fold change every 38mV, increasing as the internal potential is made negative. (8) Upon early 'repolarization of the membrane to -8OmV this voltage dependent component of 4-AP+ block proceeds exponentially with a o time constant of 8 msec. (9) The blockage of the delayed channel by 4-AP: and 4-AP+ is described 1 0 in mathematical form; and the results discussed in terms of possible molecular structures and events within the channel. (10) The repolarizingphase of the action potential is slowed in the presence of lmM 4-AP (pH 7.2). The resting potential, the r~te of rise and overshoot of the action potential are little affected. (11) The inwardly rectifying component of the potassium conductance is reduced by 4-AP. This block is intensified in alkaline solution which' suggests that the cationic form inside the cell is the active form. (12) The delayed potassium channel has also been studied ~n solutions " of different pH. At pH 5.0, gK is reduced by 16.3% and the threshold shifted by 20.2 mV in the depolarizing direction. At pH 9.8, gK is red"uced by 13% and the threshold shifted by l5mV in the depolarizing direction. (13) The delayed potassium current is abolished after treatment with 5mM 4-AP (pH 9.8). In these experiments, the transient current which remains is associated with the charging of the membrane capacity. (14) Asymmetries in the membrane capacity are observed, similar to those described by Schneider and Chandler (1973). These asymmetries are thought to be intra membrane currents associated \-lith exitation contraction ~ coupling. Formaldehyde, which interrupts exitation contraction coupling, reduces the asymmetry in the membrane capacity.

Plants growing in arid regions often suffer from high shoot temperatures, low shoot water concentrations, low turgor pressures, and high salinity in the rhizosphere. To investigate which traits confer tolerance on plants in these areas a range of genotypes was studied. These included Local (an uncharacterized landrace grown in south western Pakistan), Soorab-96 and Awaran-2002 (both elite cultivars developed by ICARDA and commercially grown in Pakistan), and Optic (an elite European cultivar). Measurements on germination, growth, and yield suggested that landrace Local is significantly least affected by high salinity (p<0.05) compared with lines Soorab-96, Awaran-2002 and Optic. Further investigations on ion profiling established that landrace Local could maintain low Na+/K+ ratios. This appeared to arise from Local’s ability to prevent Na+ accumulation in the roots and shoots by enhanced exclusion or efflux or both. Probably this unique characteristic of landrace Local helped in maintaining its photosynthetic efficiency, plant water status, and stomatal conductance, which resulted in its better performance and survival in high salinity. There was no evidence that high tissue solute concentrations, high proline levels or life cycle strategies played a role in salt stress tolerance. In addition, there was no evidence that osmotic stress was responsible for the observed suppression of growth in any of the genotypes. The main conclusion from this study is that for glycophytes (which do not complete a full life cycle above 100 mM NaCl; this includes all of the world’s major crops), it is the ionic component of salinity stress that impairs growth processes and yield, not the osmotic component. Further research on salinity stress in crops should focus on understanding the processes that control ionic balance rather than osmoregulation. There is some evidence that long term exposure of plants in the preceding generations to moderately high salt concentrations (e.g. 100 mM NaCl) improves barley halotolerance in succeeding generations, i.e. halotolerance has a transgenerational, epigenetic basis, but there was also evidence that the improved halotolerance in the Local genotype was partly genetic. In another series of experiments the importance of short periods of high leaf temperatures (Tleaf) on photosynthetic efficiency of barley genotypes Local, Optic, and Soorab-96 was investigated. In all three genotypes light saturated carbon dioxide assimilation rates (Asat) and the carboxylation coefficients (CO2, a measure of the efficiency of CO2 fixation) in the fourth fully expanded leaves were equally suppressed to approximately 20 % of their pre-treatment levels immediately after a short period of heat stress (Tleaf > 40.0 ± 0.5 °C for 20 minutes). Parallel measurements using a range of techniques confirmed that the suppression of Asat and CO2 was not attributable to changes in the light harvesting capacity (leaf absorptance and chla excitation spectra), maximum quantum efficiency of PSII (PSII, Fv/Fm), and to stomatal conductance (gs). It is unlikely that the suppression arose from damage to the electron transport chain¸ or to the capacity to develop or maintain non-photochemical quenching (NPQ, which is dependent on the transthylakoid pH), but these possibilities cannot be dismissed. LC-MS and enzymic analysis of leaf metabolite levels showed that the pools of metabolites feeding into RuBisCO are not affected by heat stress whilst those of the metabolites flowing away from RuBisCO were significantly depleted. The implication is that short periods of heat stress severely impairs RuBisCO, RuBisCO Activase, or processes close to the carboxylation step. Five days after heat stress Asat and CO2 had significantly recovered to approximately 40 % (p<0.05) of their pre-stress levels in landrace Local, but no significant recovery was observed in any of the elite lines including those distributed by ICARDA for arid land production. These findings provide evidence that thermal damage may play a significant role in yield suppressions in arid regions and that there is a genetic basis for thermotolerance in barley.

The compartmentalisation of cAMP/PKA signalling pathway within specific regions of the cell plays a critical role to achieve the specificity of response. Adenylyl cyclases (AC) are localised at discrete regions of the plasma membrane and phosphodiesterases (PDEs), the only enzymes that degrade cAMP, have been shown to be pivotal in generating spatially restricted pools of cAMP, therefore underpinning spatial control of this second messenger signal. In addition, A-kinase anchoring proteins (AKAPs) are of key importance as they anchor PKA in proximity of its specific targets, thus favouring target selective phosphorylation. Such organisation leads to local activation of PKA subsets through the generation of confined intracellular gradients of cAMP. Interestingly it has been shown that AKAP450 localises to the centrosome, the major microtubule-organising centre, where it functions as a ‘multi-scaffolding’ protein by simultaneously associating PKA with PDE4D3 as well as other kinases and phosphatases. Beside this a large body of evidence suggests that the centrosome is essential for the regulation of the cell cycle progression by acting as a scaffold protein for a network of signalling pathways which in turn trigger cellular division. In the past few years the development of FRET-based sensors has allowed the study of cAMP dynamics with high spatial-temporal resolution. By using this approach it is now possible to monitor real-time fluctuations of cAMP and PKA activity in distinct subcellular compartments and to investigate their physiological role. The aim of the research presented in this dissertation is to exploit FRET-based sensor to investigate the signalling of cAMP at the centrosome and to define the role of PDE4D3 anchored to AKAP450 in shaping a cAMP pool in such specific compartment. The centrosomal AKAP450/PKA/PDE4D3 macromolecular complex may play a role in the control of cell cycle progression. To this purpose a CHO clone stably expressing the FRET sensor based on PKA was generated. As expected fluorescence microscopy analysis of this clone indicated that the sensor anchors to endogenous centrosomal AKAPs. Further real-time imaging of basal cAMP provided evidence that the centrosome is a domain with lower cAMP concentration as compared to the bulk cytosol and that PDE4D3 activity is required to maintain a low cAMP level in the centrosomal area. Interestingly the same cells challenged with the cAMP raising agent forskolin show a larger FRET change at the centrosome as compared to the bulk cytosol. By using the unimolecular FRET EPAC-based sensor for cAMP, targeted to the centrosome, it was possible to exclude that the level of cAMP generated at the centrosome by forskolin was higher than the level of cAMP generated in the cytosol. Thus, it has been hypothesised that anchoring of PKA to AKAP450 lowers the activation constant of the enzyme leading to a higher FRET change at the centrosome as compare to the bulk cytosol. This hypothesis has been confirmed by expressing in the cytosol the fragment of AKAP450 that anchors PKA and by showing that binding of PKA to the cytosolic fragment also results in increased sensitivity of the enzyme to cAMP. Eventually analysis of PKA activity, by using a FRET-based A-kinase activity reporter (AKAR), indicated that anchoring of PKA to the cytosolic fragment of AKAP450 accounts also for an increased PKA activity. The molecular mechanism involved in the increased sensitivity of PKA-bound to AKAP450 was also investigated. Interestingly anchoring of PKA to AKAP450 increases the auto-phosphorylation of PKA. Generation of a non-phosphorylatable version of PKA-RII subunit (mutRII) and further generation of a CHO clone stably expressing the mutPKA FRET based sensor strongly indicates that the high sensitivity of PKA bound to AKAP450 is mediated by the auto-phosphorylation site and more specifically the binding of PKA to AKAP450 seems to favour the auto-phosphorylation of PKA. Finally the role of AKAP450/PKA/PDE4D3 macromolecular complex in the regulation of cell cycle progression was analysed. Displacement of endogenous PDE4D3 from the centrosome by over-expression of a catalytically dead version of PDE4D3 (dnPDE4D3), results not only in the abolishment of difference in cAMP concentration between centrosome and cytosol, but also in an altered cell cycle progression, suggesting that PDE4D3 plays a key role in the regulation of the cell cycle. In conclusion this study provided evidence for a novel mechanism by which anchoring of PKA to AKAPs modulate the activation constant of the enzyme, thereby providing a mean to regulate enzyme activity locally.

The ability of cells to respond correctly to signals from their microenvironment is an essential prerequisite of life. Many external signals are detected through G protein-coupled receptor (GPCR) signalling pathways, which control all aspects of eukaryotic physiology. Ligand-bound GPCRs initiate signalling by promoting exchange of GDP for GTP on the Gα subunit of heterotrimeric G proteins, thereby facilitating activation of downstream effectors. Signalling is terminated by the hydrolysis of GTP to GDP through intrinsic GTPase activity of the Gα subunit, in a reaction catalysed by the regulator of G protein signalling (RGS) proteins. Due to the problem of complexity in higher eukaryotic GPCR signalling, the matingresponse in Schizosaccharomyces pombe has been used to study GPCR signalling in isolation. In vivo data from quantitative assays of reporter strains and live-cell uorescence microscopy informs the development of an ordinary differential equation model of the signalling pathway, first described by Smith et al., 2009. The rate of nucleotide exchange on the Gα (Gpa1) is a key molecular mechanism controlling duration and amplitude of signalling response. The in uence of this is investigated through characterisation of Gpa1 nucleotide exchange mutants and perturbation of reaction rate parameters in the computational model. Further, this thesis also presents data relating to the temporal and spatial regulation of Rgs1 (the sole RGS protein for Gpa1). Using an inter-disciplinary approach, evidence is provided to suggest that an interaction between Rgs1 and the C-terminal tail of the GPCR (Mam2) tethers Rgs1 to the plasma membrane to facilitate its function. Finally, quantification of signalling at the single cell level is described. Time-lapse livecell imaging of uorescent reporter cells is optimised and single cell signalling response quantified using image analysis software. Single cell quantification provides greater insight into temporal dynamics, cell-to-cell variability, and highlights the existence of mechanisms for cellular decision-making.

Chemerin is a newly identified adipokine and exerts its functional effects by binding to its natural GPCR, known as CMKLR1. Chemerin is highly expressed in the adipose tissue and in lower levels in other body tissues; and is known to play an important role in adipocyte differentiation and metabolism. Chemerin circulates at the normal physiological concentrations of approximately 3-4nM in humans, and circulating chemerin levels positively correlate with various facets of metabolic abnormalities; such as insulin resistance, type 2 diabetes, high triglycerides, hypertension, and associated risks of development of diseases of cardiovascular system. Endothelial Cells (ECs) line the vasculature of the entire circulatory system and form a direct contact with the bloodstream. In this project, the role of chemerin in EC biology was proposed, and was studied in terms of activation of important signalling Mitogen-activated Protein Kinases (MAPKs) including Extracellular signal-regulated Kinase (ERK) 1/2, ERK5, p38, Stress-activated Protein Kinase/c- Jun NH2-terminal Kinase (SAPK/JNK); and Akt/Protein Kinase B (PKB) and Adenosine Monophosphate Protein Kinase (AMPK)-α in a time- and concentrationdependent manners. These signalling kinases regulate the activity of different transcription factors which then regulate the expression of different genes. Chemerin increased the expression of Hypoxia-inducible Factor (HIF)-1α, a hypoxia-inducible transcription factor which is known to regulate the Vascular Endothelial Growth Factor (VEGF) gene expression. Interestingly, VEGF165, the most potent angiogenic isoform of VEGF protein expression was down-regulated by chemerin in a concentration-dependent manner; whereas, chemerin upregulated the protein expression of VEGF165b, an opposite anti-angiogenic counterpart of VEGF165. Chemerin mediated EC proliferation, migration and capillary tube formation; which are the key processes implicated in the process of normal and pathological angiogenesis. Chemerin altered the protein expression levels of Cell Adhesion Molecules (CAMs) including E-selectin, ICAM-1 and VCAM-1 – increased the activity of Nuclear Factor (NF)–kappa (κ) B pathway – and encouraged Endothelial- Monocyte cell adhesion in a concentration-dependent manner. Nitric Oxide (NO), not only keeps the vascular health in check by downregulating the expression levels of adhesion molecules, but also acts as a potent vasodilator. Endothelial Nitric Oxide Synthase (eNOS), an enzyme constitutively expressed in the endothelial cells regulates the production of NO in the endothelium. Chemerin increased eNOS activity by causing eNOS phosphorylation at Ser1177, and dephosphorylating at Thr495 phosphorylation sites. Chemerin increased the protein expression of nonconstitutively expressed enzyme, inducible Nitric Oxide Synthase (iNOS), which is mainly induced during injury or inflammation and is known to produce 100- to 1000-times more NO compared to that of eNOS. However, interestingly, chemerin failed to show any significant changes in the amounts of combined nitrite and nitrate (NOx) levels in HMEC-1 cells; whereas, nitrite (NO2–) levels were decreased in a concentration-dependent manner.

Many high throughput sequencing protocols for RNA and DNA require that the polynucleic acid is fragmented so that the identity of a limited number of nucleic acids of one or both of the ends of the fragments can be determined by sequencing. The nucleic acid sequence allows the fragment to be located within the genome, and the fragment distribution can then be used for a variety of different purposes. In the case of DNA this includes identifying the locations where specific proteins are bound to the genome. In the case of RNA this includes quantifying the expression levels of different gene variants or transcripts. If the locations of the polynucleic acid fragments are partly determined by the underlying nucleic acid sequence this could bias any results derived from the data. Unfortunately, such sequence dependencies have already been observed in the distribution of both RNA and DNA fragments. Previous analyses of such data in order to reduce the bias have examined the role of regional characteristics such as GC bias, or the bias towards a specific sequence at the start of the fragments. This thesis introduces a new method for modelling the bias which considers the degree to which the nucleotide sequence affects the likelihood of a fragment originating at that location. This shows that there is often not a single bias characteristic, but multiple, alternative sequence biases that coexist within a single dataset. This also shows that the nucleotide sequence immediately proximal to the fragment also has a significant effect on the fragment likelihood. This new approach highlights characteristics that were previously hidden and provides a more powerful basis for correcting such bias. Multiple alternative sequence biases are observed when both RNA and DNA are fragmented, but the more detailed information provided by the new technique shows in detail how the characteristics are different for RNA and DNA and indicates that very different molecular mechanisms are responsible for the biases in the two processes. This thesis also shows how removing the effect of this bias in ChIP-seq experiments can reveal more subtle features of the distribution of the fragments. This can provide information on the nature of the binding between proteins and the DNA with per-nucleotide precision, revealed through the change in likelihood of the DNA fragmenting at each position in the binding site. It is also shown how the model fitting technique developed to analyse sequence bias can also be used to obtain additional information from the results of ChIP-chip experiments. The approach is used to find the nucleotide sequence preference of DNA binding proteins, and also the cooperative effects associated with binding at multiple binding sites in close proximity.