Phosphorylation of Exo1 modulates homologous recombination repair of DNA double-strand breaks

DNA double-strand break (DSB) repair via the homologous recombination pathway is a multi-stage process, which results in repair of the DSB without loss of genetic information or fidelity. One essential step in this process is the generation of extended single-stranded DNA (ssDNA) regions at the break site. This ssDNA serves to induce cell cycle checkpoints and is required for Rad51 mediated strand invasion of the sister chromatid. Here, we show that human Exonuclease 1 (Exo1) is required for the normal repair of DSBs by HR. Cells depleted of Exo1 show chromosomal instability and hypersensitivity to ionising radiation (IR) exposure. We find that Exo1 accumulates rapidly at DSBs and is required for the recruitment of RPA and Rad51 to sites of DSBs, suggesting a role for Exo1 in ssDNA generation. Interestingly, the phosphorylation of Exo1 by ATM appears to regulate the activity of Exo1 following resection, allowing optimal Rad51 loading and the completion of HR repair. These data establish a role for Exo1 in resection of DSBs in human cells, highlighting the critical requirement of Exo1 for DSB repair via HR and thus the maintenance of genomic stability.

Mathematical modelling of soft callus formation in early murine bone repair

Fracture healing is a complicated coupling of many processes. Yet despite the apparent complexity, fracture repair is usually effective. There is, however, no comprehensive mathematical model addressing the multiple interactions of cells, cytokines and oxygen that includes extra-cellular matrix production and that results in the formation of the early stage soft callus. This thesis develops a one dimensional continuum transport model in the context of early fracture healing. Although fracture healing is a complex interplay of many local factors, critical components are identified and used to construct an hypothesis about regulation of the evolution of early callus formation. Multiple cell lines, cellular differentiation, oxygen levels and cytokine concentrations are examined as factors affecting this model of early bone repair. The model presumes diffusive and chemotactic cell migration mechanisms. It is proposed that the initial signalling regime and oxygen availability arising as consequences of bone fracture, are sufficient to determine the quantity and quality of early soft callus formation. Readily available software and purpose written algorithms have been used to obtain numerical solutions representative of various initial conditions. These numerical distributions of cellular populations reflect available histology obtained from murine osteotomies. The behaviour of the numerical system in response to differing initial conditions can be described by alternative in vivo healing pathways. An experimental basis, as illustrated in murine fracture histology, has been utilised to validate the mathematical model outcomes. The model developed in this thesis has potential for future extension, to incorporate processes leading to woven bone deposition, while maintaining the characteristics that regulate early callus formation.

Reduced excision repair cross-complementing 1 expression associates with enhanced papilloma formation and fibroblast transformation after genetic disruption of secreted protein acidic and rich in cysteine

SPARC (secreted protein acidic and rich in cysteine)/ osteonectin/BM-40 is a matricellular protein implicated in development, cell transformation and tumorigenesis. We have examined the role of SPARC in cell transformation induced chemically with 7,12-dimethylbenz[a]anthracene (DMBA) and 12- tetradecanoylphorbol-13-acetate (TPA) in embryonic fibroblasts and in the skin of mice. Embryonic fibroblasts from SPARCnull mice showed increases in cell proliferation, enhanced sensitivity to DMBA and a higher number of DMBA/TPA-induced transformation foci. The number of DMBA-DNA adducts was 9 times higher in SPARCnull fibroblasts and their stability was lower than wild-type fibroblasts, consistent with a reduction in excision repair cross-complementing 1 the nucleotide excision repair enzyme in these cells. The SPARCnull mice showed an increase in both the speed and number of papillomas forming after topical administration of DMBA/TPA to the skin. These papillomas showed reduced growth and reduced progression to a more malignant phenotype, indicating that the effect of SPARC on tumorigenesis depends upon the transformation stage and/or tissue context. These data reinforce a growing number of observations in which SPARC has shown opposite effects on different tumor types/stages.

In Situ Observation of the Thermal Decomposition of Weddelite by Heating Stage Environmental Scanning Electron Microscopy

The morphological and chemical changes occurring during the thermal decomposition of weddelite, CaC2O4·2H2O, have been followed in real time in a heating stage attached to an Environmental Scanning Electron Microscope operating at a pressure of 2 Torr, with a heating rate of 10 °C/min and an equilibration time of approximately 10 min. The dehydration step around 120 °C and the loss of CO around 425 °C do not involve changes in morphology, but changes in the composition were observed. The final reaction of CaCO3 to CaO while evolving CO2 around 600 °C involved the formation of chains of very small oxide particles pseudomorphic to the original oxalate crystals. The change in chemical composition could only be observed after cooling the sample to 350 °C because of the effects of thermal radiation.

Experiences with an Object-Oriented, Multi-Stage Language

Metaphor is a multi-stage programming language extension to an imperative, object-oriented language in the style of C# or Java. This paper discusses some issues we faced when applying multi-stage language design concepts to an imperative base language and run-time environment. The issues range from dealing with pervasive references and open code to garbage collection and implementing cross-stage persistence.

Particle and gaseous emissions from commercial aircraft at each stage of the landing and takeoff cycle

A novel technique was used to measure emission factors for commonly used commercial aircraft including a range of Boeing and Airbus airframes under real world conditions. Engine exhaust emission factors for particles in terms of particle number and mass (PM2.5), along with those for CO2, and NOx were measured for over 280 individual aircraft during the various modes of landing/takeoff (LTO) cycle. Results from this study show that particle number, and NOx emission factors are dependant on aircraft engine thrust level. Minimum and maximum emissions factors for particle number, PM2.5, and NOx emissions were found to be in the range of 4.16×1015-5.42×1016 kg-1, 0.03-0.72 g.kg-1, and 3.25-37.94 g.kg-1 respectively for all measured airframes and LTO cycle modes. Number size distributions of emitted particles for the naturally diluted aircraft plumes in each mode of LTO cycle showed that particles were predominantly in the range of 4 to 100 nm in diameter in all cases. In general, size distributions exhibit similar modality during all phases of the LTO cycle. A very distinct nucleation mode was observed in all particle size distributions, except for taxiing and landing of A320 aircraft. Accumulation modes were also observed in all particle size distributions. Analysis of aircraft engine emissions during LTO cycle showed that aircraft thrust level is considerably higher during taxiing than idling suggesting that International Civil Aviation Organization (ICAO) standards need to be modified as the thrust levels for taxi and idle are considered to be the same (7% of total thrust) [1].

User-designer collaboration during the early stage of the product development process

As an understanding of users' tacit knowledge and latent needs embedded in user experience has played a critical role in product development, users’ direct involvement in design has become a necessary part of the design process. Various ways of accessing users' tacit knowledge and latent needs have been explored in the field of user-centred design, participatory design, and design for experiencing. User-designer collaboration has been used unconsciously by traditional designers to facilitate the transfer of users' tacit knowledge and to elicit new knowledge. However, what makes user-designer collaboration an effective strategy has rarely been reported on or explored. Therefore, interaction patterns between the users and the designers in three industry-supported user involvement cases were studied. In order to develop a coding system, collaboration was defined as a set of coordinated and joint problem solving activities, measured by the elicitation of new knowledge from collaboration. The analysis of interaction patterns in the user involvement cases revealed that allowing users to challenge or modify their contextual experiences facilitates the transfer of knowledge and new knowledge generation. It was concluded that users can be more effectively integrated into the product development process by employing collaboration strategies to intensify the depth of user involvement.

The impact of perceived stage of cancer on carers’ anxiety and depression during the patients’ final year of life

Objective: This paper explores the effects of perceived stage of cancer (PSOC) on carers' anxiety and depression during the patients' final year. Methods: A consecutive sample of patients and carers (N=98) were surveyed at regular intervals regarding PSOC, and anxiety and depression using the Hospital Anxiety and Depression Scale. Means were compared by gender using the Mann-Whitney U-test. The chi-square was used to analyse categorical data. Agreement between carers' and patients' PSOC was estimated using kappa statistics. Correlations between carers' PSOC and their anxiety and depression were calculated using the Spearman's rank correlation. Results: Over time, an increasing proportion of carers reported that the cancer was advanced, culminating at 43% near death. Agreement regarding PSOC was fair (kappa=0.29-0.34) until near death (kappa=0.21). Carers' anxiety increased over the year; depression increased in the final 6 months. Females were more anxious (p=0.049, 6 months; p=0.009, 3 months) than males, and more depressed until 1 month to death. The proportion of carers reporting moderate-severe anxiety almost doubled over the year to 27%, with more females in this category at 6 months (p=0.05). Carers with moderate-severe depression increased from 6 to 15% over the year. Increased PSOC was weakly correlated with increased anxiety and depression. Conclusions: Carers' anxiety exceeded depression in severity during advanced cancer. Females generally experienced greater anxiety and depression. Carers were more realistic than patients regarding the ultimate outcome, which was reflected in their declining mental health, particularly near the end.

Parametric building development during early design stage

Objectives The objectives of this project were two-fold: • Assess the ease with which current architectural CAD systems supported the use ofparametric descriptions in defining building shape, engineering system performance and cost at the early stages of building design; • Assess the feasibility of implementing a software decision support system that allowed designers to trade-off the characteristics and configuration of various engineering systems to move towards a “global optimum” rather than considering each system in isolation and expecting humans to weigh up all of the costs and benefits. The first stage of the project consisted of using four different CAD systems to define building shells (envelopes) with different usages. These models were then exported into a shared database using the IFC information exchange specifications. The second stage involved the implementation of small computer programs that were able to estimate relevant system parameters based on performance requirements and the constraints imposed by the other systems. These are presented in a unified user interface that extracts the appropriate building shape parameters from the shared database Note that the term parametric in this context refers to the relationships among and between all elements of the building model - not just geometric associations - which will enable the desired coordination.

Final report: stage 1 : results

This research project aims to improve economic, social and environmental sustainability of the pre-cast concrete and construction and demolition waste supply chains through the development, trial and evaluation of an innovative supply chain management strategy. The long-term goals are to improve competitive behaviour and market sector performance and improve business process efficiency and effectiveness of public sector program delivery by influencing policy development, changing organisational behaviour and implementation development to achieve more economic, social and environmental sustainable markets.