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The following thesis is a composite of two separate research projects which were undertaken by the author for the award of an MRes in Molecular and Cellular Biology within the School of Biosciences at the University of Birmingham. Part one of this thesis will detail the first research project which sought to characterise the contribution of the enzyme phospholipase B to the intercellular lifecycle employed by the pathogenic fungus Cryptococcus neoformans which has the ability to survive within the phagolysosome of immune cell macrophages. This project used cell culture and microscopy techniques as well as whole cell lipidomic analysis and found that many aspects of Cryptococcus neoformans parasitism of macrophages are modified by phospholipase B activity. Part two of this details the second project which examined the predatory bacteria Bdellovibrio bacteriovorous. This bacterium has a unique lifecycle which involves predation of other gram negative bacteria resulting in prey cell invasion and an interperiplasmic growth and replication phase. This project sought to purify and characterize two B. bacteriovorous C-di-GMP modifying enzymes – Bd2325 and Bd1971. Herein we report the first putative analyses of these proteins.

Ground penetrating radar (GPR) technology has existed for many decades, but it has only been in the last 20 to 30 years that it has undergone great development for use in near surface ground investigations. The early 1980's saw the first major developments in the application of GPR for pavements (i.e. engineered structures designed to carry traffic loads), and it is now an established investigation technique, with generic information included in several national standard guidance documents. Analysis of GPR data can provide information on layer depths, material condition, moisture, voiding, reinforcement and location of other features. Assessing the condition of pavements, in order to plan subsequent maintenance, is essential to allow the efficient long-term functioning of the structure and GPR has enhanced and improved the range and certainty of information that can be obtained from pavement investigations. Despite the recent establishment of the technique in pavement investigation, the current situation is one in which GPR is used routinely for pavement projects in only a minority of countries, and the specialist nature of the technique and the sometimes variable results that are obtained can mean that there is both a lack of appreciation and a lack of awareness of the potential information that GPR can provide. The fact that GPR is still a developing technique, and that many aspects of its use are specialised in their nature, means that there are also several technical aspects of GPR pavement investigations which have not been fully researched, and knowledge of the response of GPR to some material conditions has not been fully established. The overall aim of this EngD research project was to provide improved pavement investigation capabilities by enhancing the methodologies and procedures used to obtain information from GPR. Several discrete research topics were addressed through various research methods including a literature review, fieldwork investigations, experimental laboratory investigations and a review of previously collected data. The findings of the research allowed conclusions and recommendations to be made regarding improved fieldwork methodologies, enhancing information and determining material condition from previously collected GPR data, assessing the effect of pavement temperature and moisture condition on GPR data and also on managing errors and uncertainty in GPR data. During the EngD project, a number of documents and presentations have been made to publicise the findings both within the EngD sponsoring company (Jacobs) and externally, and an in-house GPR capability has been established within Jacobs as a direct result of the EngD project.

This thesis uses a combination of industrially acquired seismic reflection data, well data, topographic data and satellite imagery to investigate the structure, evolution and geophysical expression of extrusive constructions found within large (-500 m diameter) mud volcano systems from the South Caspian Basin. The principal aim is to gain a better understanding the structural architecture of mud volcano systems and the ways in which they are constructed. To this end this thesis includes three core research chapters which present investigations into the internal structure and eruptive history of a large mud volcano system, the geophysical response of seismic data to gassy seabed conditions and the structure and formation of mud volcanic subsidence craters. In the first core chapter the edifice of the giant C'hirag mud volcano system was investigated using three-dimensional (3D) seismic data. Internally, this feature consists of a number of discrete seismic facies units interpreted to represent either wedge-shaped units of erupted mud volcanic sediment or sheet-like units of non-eruptive sediment. Unit stacking patterns indicate the importance of pulsed mud volcanic activity as a control on the internal architecture of large mud volcano edifices and suggest it to be an important mechanism of basinal sediment and fluid expulsion. Analysis of the geometrical relationships of the internal sediment units to an underlying collapse caldera allows for a reconstruction of the system's history of collapse. Together, the details of internal unit type, stacking and relative edifice collapse timing constitute a detailed reconstruction of the volcano system's eruptive history and a record of the structural evolution of a large focussed fluid flow system. At the seabed a number of volcano systems within the South Caspian Sea study area were found to be imaged by areas of phase-reversed seabed reflection in seismic data. These "seabed phase reversals" are useful for better delimiting and understanding the structure of mud volcano source points and the extent of recent eruptive deposits. At one example kilometre-scale lobate mudflows are seen emerging from two seabed mud pool (salses) emphasizing the importance of both features in shaping the volcano's seabed morphology. Testing the hypothesis that seabed phase reversals are the result of gas within the seabed sediment took the form of a one-dimensional geophysical model of the study area seabed constructed using data from a borehole together with other published data. The results revealed that a phase reversal of the seabed reflection is a geophysical possibility under conditions typical of gassy seabed sediment. There is therefore a high likelihood that seabed phase reversals are the result of gas within seabed sediment. It is therefore suggested that seabed phase reversals can be used alongside other acoustic phenomena that indicate the presence of gas in a sedimentary section. In the final core chapter circular craters found at the upper terminations of onshore and offshore mud volcano systems are investigated. Using field maps. seismic lines, topographic data and satellite images it has been possible to describe these craters in detail for the first time and compile a generalized model for their structure. This includes a crater rim, an inward dipping crater margin fault, a moat and raised crater pedestal of freshly extruded mud volcanic sediment. The characteristic "moat and pedestal" morphology features at most of the craters featured here as well as at a number of others from elsewhere. Whilst the precise mechanism of crater formation is unclear it is strongly suspected that they form as a result of subsurface evacuation and collapse. They are thus similar to other sedimentary and igneous collapse features for which they may be useful analogues.