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End-binding proteins (EBs) are specialised proteins that can autonomously track growing microtubule ends whilst recruiting other proteins (+TIPs). By interacting with STIM1, a transmembrane protein associated with the endoplasmic reticulum (ER), EBs are able to mediate ER re-organisation and tubulation. Intracellular transport is vital for achieving the correct distribution of organelles. This work aims to derive an analytical model that can explain how transiently binding proteins can couple microtubule growth to the motion of cargo inside cells. It will be shown in this work that EBs exhibit a dwell time distribution that is best _t by a superposition of two exponential decay functions, which indicates multistate binding behaviour. An analytical model has been developed that reproduces these binding dynamics. Once expanded to study cargo permanently bound to multiple EBs, this model is able to predict the phenomenon of tip tracking as a response to position dependence in the EB-microtubule binding rate distribution. Using experimentally-derived input parameters, it will be shown that the resulting effective velocity exhibited by cargo acts towards the growing ends of microtubules and can be of similar magnitude to the microtubule growth velocity. Simulated cargo exhibit the same qualitative behaviour as multivalent cargo studied in vitro. Finally, it will be shown that cargo-EB interactions act to inhibit the tip tracking capabilities of cargo by reducing their average dwell time and the magnitude of their effective velocity. This work details one method by which cells can utilise the stochasticity of individual protein dynamics to generate predictable large scale behaviour.

The mammalian target of rapamycin (mTOR) regulates cell growth and proliferation in response to nutrients and growth factors. The role of mTOR in the biology of embryonic stem cells has not been extensively characterised. The principle aim of this research was to assess the feasibility of manipulating the mTOR pathway to provide bioprocessing improvements for the expansion and differentiation of embryonic stem cells. In order to achieve this aim, the cellular distribution and localisation of mTOR pathway phosphoproteins was assessed and the effect of pathway inhibition on ES cell proliferation and viability was characterised. The key findings of this study revealed that in mouse ES cells, mTOR pathway proteins were phosphorylated during mitosis. Secondly, inhibition of mTOR in growth factor-stimulated pluripotent stem cells impaired proliferation but not viability. Upon withdrawal of growth factors, cells lost their compact shape and exhibited a spread morphology. Under these conditions mTOR inhibition reduced the viability and proliferation of ‘compact’ cells but not ‘spread’ cells. Thus, during the expansion of ES cells the mTOR pathway may be stimulated. During early differentiation, inhibition of the pathway may improve the purity of the final cell preparation and reduce the prevalence of parent stem cells. In conclusion, the experimental findings discussed here show that temporal manipulation of the mTOR pathway in embryonic stem cells may provide bioprocessing advantages resulting in an increased yield of parent cell populations during expansion and increased purity of differentiated cells. The sensitivity of the mTOR pathway to the bioavailability of nutrients may offer a cost-effective route to optimising cell production in an industrial scale process. Further work to elucidate the role of the mTOR complex 2 in ES cell proliferation may provide an additional level of control to independently modulate cell proliferation and growth during expansion and differentiation.

Interstitial Free (IF) steels are highly formable, ultra low carbon/nitrogen strip grades containing titanium and/or niobium to remove interstitial elements from solution. They are typically used for severe forming operations such as oil sumps in cars. However, these steels typically have proof stresses of 150-170MPa. With the addition of solid solution strengthening elements, they can be used to form complex structural components for the automotive industry. Phosphorus is commonly used to provide solid solution strengthening, since small additions lead to a significant increase in strength. However, phosphorus additions have been identified as a potential cause of Cold Work Embrittlement (CWE). CWE is a phenomenon whereby a formed component fails in a brittle manner during a secondary working operation (e.g. impact or redraw). The problem has been attributed to the segregation of phosphorus to grain boundaries and has mainly been observed in laboratory impact tests on high phosphorus IF steels. The potential for CWE to occur has attracted world-wide concern from steelmakers and steelusers, but no in-service failures have been reported and the commercial significance of this phenomenon is still not clear. The work detailed in this thesis involves study of the techniques used to measure embrittlement and developing an understanding of the fracture mechanisms involved. The literature review details the metallurgy, production and processing of IF steels as well as a discussion of CWE. The experimental work includes a detailed evaluation of the current test techniques, including the effects of varying key test parameters on the susceptibility to brittle fracture. Work is also presented on compositional and processing effects, including the use of Atom Probe Field Ion Microscopy to study grain boundary segregation. Finally, a small sample test, developed for use in the power industries, is used to study CWE susceptibility.

As early as the mid 1960's the production and scheduling systems at the Port Talbot and Llanwern sites of British Steel were computerised. This involved real-time shop floor data collection systems enabling material tracking and stock/order analysis. All orders were handled by computer systems. This enabled the scheduling sections to plan and schedule orders through the various processes aiming to meet delivery promises and control stocks. Each item of plant was scheduled individually, supplying adequate stock for the next process. Also, the planning and scheduling systems for Port Talbot were different and separate to Llanwern. In January 1995 work started on enhancing both works' planning and scheduling systems leading towards one common system. Initially the planning systems were developed to each site followed by the new scheduling systems. The most fundamental difference in the new system is that it plans the production activities for the whole plant, rather than just the individual units. This thesis describes the old planning and scheduling systems within Port Talbot and Llanwern Works and the difficulties associated with the old, manual methods used for scheduling the production units, particularly the steelmaking/continuous casting plant and the hot strip mills. Descriptions of the newly adopted systems are given with details of the implementations, plus information on the problems encountered. Associated systems are also described, in particular the manufacturing execution system (MES) and the plans for replacing it with a new system. There is also a comprehensive review of the literature pertaining to planning and scheduling in the metals, and more specifically, the steel industry.

Both aggressive mitigation strategies and negative emission technologies are required to limit global warming to 2 ◦ C. Tropical forest restoration is widely seen as a potential way to achieve negative emissions. Yet its maximum potential and the carbon cycle response to it have not been quantified. This PhD starts by looking at the only comparable large scale reforestation event in human history - the cessation of agriculture caused by the epidemics-driven deaths of 90 % of the indigenous population of the Americas after 1492 CE. I quantify the magnitude of vegetation regrowth and carbon uptake after European arrival in the Americas (55.8 million ha and 7.4 Pg C respectively) based on published population, land use, and biomass estimates. This is compared to the observed changes in climate and the carbon cycle at the time. Given the uncertainty in the observations, a series of idealised experiments are performed with an Earth System Model (CESM). These show a high sensitivity of the carbon cycle impact to the land use reconstruction used and that factorial forcing experiments would be required to conclusively determine the impact of the 1492 CE land use change. To better understand the Earth system response to large scale tropical forest restoration such an experiment is performed with a state-of-the-art Earth System Model. An experiment where all land use in the tropics (1,815 million ha) is rapidly stopped under an aggressive mitigation scenario (RCP 2.6) is performed with HadGEM2-ES. The resulting secondary succession results in a small CO2 (∼9.5 ppm) reduction by 2100 CE, but does not translate to a detectable decline in global temperature. Furthermore, negative carbon cycle feedbacks offset 65% of the benefits from terrestrial carbon uptake. I conclude that reforestation alone is insufficient to provide the substantial negative emissions.

The restoration of degraded tropical lands can lead to carbon sequestration, which can mitigate climate change, alongside safeguarding biodiversity and providing other co-benefits. Recently tropical countries have pledged to restore millions of hectares of degraded lands to forest. However, important gaps in policy-facing knowledge remain. To address these I firstly assessed the rate that naturally regenerating forests sequester carbon, by systematically reviewing studies measuring forest recovery following the abandonment of agricultural lands. I found a mean above-ground carbon sequestration rate of 2.5 Mg C ha⁻¹ yr⁻¹ (± 0.6, 95% CI) over 100 years, which was not dependent on prior land use (n=71 studies). Next, I measured the results of active restoration of tropical forest, via fire exclusion and planting native seedlings, on abandoned agricultural land in Kibale National Park, Uganda. Above-ground carbon sequestration was 1.9 Mg C ha⁻¹ yr⁻¹ (± 0.4; n=50 x 0.05 ha permanent sample plots) and tree species richness (≥10 cm diameter at breast height) increased from 0 to 5 species per plot in the first 18 years after restoration (1995-2013). I then measured the results of active restoration of tropical forest via planting native seedlings and climber cutting, in selectively logged forest in Sabah, Borneo. Restored forest sequestered aboveground carbon twice as fast as selectively logged control forest (3.3±0.9 and 1.6±0.8 Mg C ha⁻¹ yr⁻¹, respectively; 24 x 0.2 ha plots, half restored, half controls) over eight years (2007-2015), and had higher tree species richness (48 and 35 species ≥10 cm DBH per plot, respectively). Lastly, I estimate the impact of fulfilling the global aspiration of restoring 350 million ha of tropical lands to forest by combining restoration pledges (including the proportion of land committed to native forest and forms of tree-based agriculture), with sequestration rates. Implementation would remove 0.4 Pg C yr⁻¹ from the atmophere over the next 100 years. Restoration is therefore shown to offer climate-relevant sequestration potential, and if active restoration is used then these future forests can be designed to optimise multiple benefits to humanity.

Biological diversity and ecosystem functions, such as the production of wood and the storage of carbon, are important ecological attributes, but how are they related? Tropical forests are the most diverse terrestrial ecosystems and key players in global carbon cycling, so preserving both functions are important conservation goals. Yet little is known about diversity–function relations here. I investigate tree diversity–function relations in African and South American old-growth tropical forests, using 323 forest plots (mostly 1-ha) from a pan-tropical network sampled using standardised techniques. I focus on aboveground biomass (AGB) and coarse woody production (AGWP). I develop methods to deal with issues that arise in calculating AGWP over long time-spans and in estimating diversity when only some individuals are identified. Diversity–function relations are assessed using two main approaches. Firstly, I use linear models to assess whether AGB and AGWP covary with diversity across large spatial extents. These models include climate and soil variables that may drive AGB and AGWP to statistically account for these, and filters to account for spatial autocorrelation. There is no evidence of a relationship between diversity and AGB. For AGWP, there is a positive relationship with genus and family-level diversity in South America, but not in Africa. Secondly, I investigate whether diversity is related to AGB or AGWP within the plots, thereby removing environmental differences among plots. Using mixed effects models on 0.04-ha subplots again shows AGB is unrelated to diversity. However, AGWP is positively associated with diversity in both continents, with a doubling of species richness increasing wood production by 11%. Taken together the results represent the first evidence of widespread positive diversity–productivity relations across the two largest tropical forest continents. The lack of positive association between diversity and biomass implies a trade-off between the conservation of tropical biodiversity and carbon storage.

The carbon stored in vegetation varies spatially and temporally due to a complex mix of anthropogenic, climatic and edaphic variables. Thus, the success of climate change policy developments such as REDD+ (Reducing Emissions from Deforestation and Forest Degradation) relies heavily on measuring and understanding this variation in the past, present and future. Here, I first analyse the change in forest cover within a 33.9 million hectare tropical study area in eastern Tanzania. I develop both linear and non-linear baselines of deforestation, providing evidence that Tanzanian forest policy has resulted in forest transition. I then present an Intergovernmental Panel on Climate Change (IPCC) ‘Tier 2’ reporting-compliant look-up method to estimate regional carbon storage, and associated 95% confidence intervals (CI). Applying this method to my study area indicates that 1.58 (95% CI: 1.56-1.60) Pg of aboveground live carbon (ALC) was stored across the landscape in the year 2000. Combining these Tier 2-type values with the historical land use/cover data I derived, I estimate that my study area had a total committed carbon release of 0.94 (0.37-1.50) Pg C between 1908 and 2000. However, look-up methods are overly simplistic for heterogeneous landscapes. Using regression equations, including the effects of disturbance, my IPCC ‘Tier 3’ compliant estimate for the same region in the year 2000 is 1.32 (0.89-3.16) Pg ALC. The most influential variables of carbon storage in the region are human, the strongest impact variables being the nature of the local governance regime (land under national control contained only 40-65% of the ALC stored in areas under local control) and historical logging (areas that had previously experienced logging held 51-77% of the ALC of never-logged areas). Throughout, I provide spatially explicit estimates to aid decision-makers who, due to the influence of anthropogenic variables, could significantly affect landscape carbon storage across this important area.

Understanding the impacts and synergies of the many threats facing tropical forests is a key research challenge. Here, three potential threats are addressed: drought, fire and lianas. Using a network of 31 plots, changes attributed to these threats are addressed over two decades in Ghanaian forests. Ghana experienced a multi-decade drought beginning in the early 1970s. The impact of this drought on functional composition and forest structure was tested. The results show clear shifts in functional composition. Despite this, biomass increased during the study period. This suggests that shifting species composition in favour of drought-tolerant species increases the resilience of tropical forests to long-term drought. A strong El Niño event in 1983 led to widespread wildfires in the Ghanaian forest zone. To test the long-term impacts of these fires the structure and composition of seven burnt plots and three control plots were compared. 27 years after initial fires, stem density and biomass were reduced in burnt plots, and composition was characteristic of disturbed forest. Over the twenty year study period, forest structure showed evidence of regeneration, but no recovery of floristic composition was observed. In contrast to the large increase in lianas observed in the Neotropics, there was only a very slight increase in the percentage of infested trees over the study period. Forest structure was found to be the main driver of liana spatial distribution. Importantly, large lianas showed different spatial patterns, as forest turnover was the strongest predictor of large liana distribution. Overall, fire was found to be the strongest threat, having a large and long-term impact on forest structure and composition. The results highlight that the prevention of fire occurrence should be a priority in tropical forest regions, as should the maintenance of biodiversity to maximise the resilience of forest to external changes.

The climate of the Neoproterozoic Snowball Earth is tested in the UKMO Unified Model, specifically the HadCM3 climate model. The model is largely left unchanged, but the boundary conditions, both external and initial, are adjusted to create experiments based on the Snowball Earth hypothesis. The model can reproduce multiple equilibrium climates, as have been seen in energy balance models of the Earth's climate. The modelled present day and Neoproterozoic versions of Earth can both reproduce both ice capped and ice covered climate states. Neither can reproduce a climate which remains ice free throughout the year, even with an equilibrated ocean or elevated levels of C02. In all cases the ice free climate reverts toward the ice capped climate after the first polar winter. The modelled Neoproterozoic ice covered climate, that is the climate of Snowball Earth, has a climate very different from the present day. These changes are mostly driven by the lower thermal inertia, latitudinal temperature differences and the changed meridional circulation that results. The weather of the modelled Snowball Earth climate is also very different, dom- inated by a strong diurnal variation due to solar heating, as opposed to the more varied weather in the present day. The model responds well to the conditions of the Snowball Earth climate, with temperatures similar to those predicted by a simple physical model. The model responds less well to high levels of C02 in the Snowball Earth climate. The ice model also allows excessive heat and moisture to escape from the ocean into the atmosphere compared to that that would be predicted from solid ice coverage of the ocean. The exit from a Snowball Earth state was also tested within the model. Neither an decrease in albedo nor an increase in CO2 is unable to increase the temperature of the climate system sufficiently to exit the Snowball Earth state.

A cross-over study is a comparitive experiment in which subjects receive a sequence of two or more treatments, one in each of a series of successive time periods, and the response of each subject is measured at the end of every period. A common problem, particularly in medicine, is that subjects fail to complete a study through dropping out during the later stages of the trial for reasons unrelated to the treatments received. Current practice is to select a design for a study on the basis of its performance under the assumption that no subjects drop out, using a criterion such as A-optimality. This is an unrealistic assumption for many medical applications. This thesis investigates how studies should be designed when it is unrealistic to assume that subjects will not drop out. A method of assessing cross-over designs is presented which judges how accurately all the pairwise treatment comparisons are estimated under the assumption that each subject has a fixed probability of dropping out during the final period, independent of treatment received and the other subjects. The method of design assessment is computationally intensive even for studies involving a relatively small number of subjects. Ways of reducing the amount of computation required are presented through establishing the link between implemented designs and a colouring problem in combinatorial theory. The reductions achieved make feasible investigations of currently used designs for cross-over studies. The results of investigations are presented for designs for the cases of particular practical importance, namely four treatment, four period and three treatment, three period studies, in which a simple carry-over model is assumed for the observations. Designs which are more robust to final period dropout than the currently favoured designs are identified.