A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.

An exploratory study on the impact of an early years' preschool intervention programme in the Republic of Ireland

Early years’ education has increasingly been identified as a mechanism to alleviate educational disadvantage in areas of social exclusion. Early years’ intervention programmes are now a common government social policy for addressing social problems (Reynolds, Mann, Miedel, and Smokowski, 1997). In particular, state provided early years’ programmes such as Head Start in the United States and Early Start in Ireland have been established to combat educational disadvantage for children experiencing poverty and socio-economic inequality. The focus of this research is on the long-term outcomes of an early years’ intervention programme in Ireland. It aims to assess whether participation in the programme enhances the life course of children at-risk of educational disadvantage. It involves an in-depth analysis of one Early Start project which was included in the original eight projects established by the Department of Education and Science in 1994. The study utilises a multi-group design to provide a detailed analysis of both the academic and social progress of programme participants. It examines programme outcomes from a number of perspectives by collecting the views of the three main stakeholders involved in the education process; students who participated in Early Start in 1994/5, their parents and their teachers. To contribute to understanding the impact of the programme from a community perspective interviews were also conducted with local community educators and other local early years’ services. In general, Early Start was perceived by all participants in this study as making a positive contribution to parent involvement in education and to strengthening educational capital in the local area. The study found that parents and primary school teachers identified aspects of school readiness as the main benefit of participation in Early Start and parents and teachers were very positive about the role of Early Start in preparing children for the transition to formal school. In addition to this, participation in Early Start appears to have made a positive contribution to academic attainment in Maths and Science at Junior Certificate level. Students who had participated in Early Start were also rated more highly by their second level teachers in terms of goal-setting and future orientation which are important factors in educational attainment. Early Start then can be viewed as providing a positive contribution to the long-term social and academic outcomes for its participants.

Urbanization effects on welfare and income diversification strategies of peri-urban farm households in Tigray, Northern Ethiopia: An empirical analysis

Urban areas in many developing countries are expanding rapidly by incorporating nearby subsistence farming communities. This has a direct effect on the consumption and production behaviours of the farm households but empirical evidence is sparse. This thesis investigated the effects of rapid urbanization and the associated policies on welfare of subsistence farm households in peri-urban areas using a panel dataset from Tigray, Ethiopia. The study revealed a number of important issues emerging with the rapid urban expansion. Firstly, private asset holdings and consumption expenditure of farm households, that have been incorporated into urban administration, has decreased. Secondly, factors that influence the farm households’ welfare and vulnerability depend on the administration they belong to, urban or rural. Gender and literacy of the household head have significant roles for the urban farm households to fall back into and/or move out of poverty. However, livestock holding and share of farm income are the most important factors for rural households. Thirdly, the study discloses that farming continues to be important source of income and income diversification is the principal strategy. Participation in nonfarm employment is less for farm households in urban than rural areas. Adult labour, size of the local market and past experience in the nonfarm sector improves the likelihood of engaging in skilled nonfarm employment opportunities. But money, given as compensation for the land taken away, is not crucial for the household to engage in better paying nonfarm employments. Production behaviour of the better-off farm households is the same, regardless of the administration they belong to. However, the urban poor participate less in nonfarm employment compared to the rural poor. These findings signify the gradual development of urban-induced poverty in peri-urban areas. In the case of labour poor households, introducing urban safety net programmes could improve asset productivity and provide further protection.

The impact of saving and credit cooperatives on food security in the West Amhara Region of Ethiopia

In rural Ethiopia, among other things, lack of adequate financial service is considered as the basic problem to alleviate rural poverty and to solve the problem of food insecurity. Commercial banks are restricted to urban centres. Providing rural financial service through RUSACCO to the poor has been proposed as a tool for economic development and for achieving food security. Evidence from research in this regard has been so far scanty, especially in rural Ethiopia. The aims of this study are to analyze the determinants of membership, to identify socioeconomic and demographic factors that influence members’ participation in RUSACCOs and to quantify the impact of RUSACCOs on member households’ food security. The study was conducted in two purposely selected woredas in the Amhara region one from food insecure (Lay Gayint woreda) and the other from food secure (Dejen woreda). Six RUSACCOs were selected randomly from these two woredas. Both qualitative and quantitative data were collected. Key informant interviews, focus group discussions and survey techniques were used to collect primary data. Collected data was then analyzed using mixed methods depending on the nature of data. For quantitative data analysis appropriate statistical models were used. The study result reveals that the number of members in each RUSACCO is very small. However, the majority of non-member respondents are willing to join RUSACCO. Lack of information about the benefits of RUSACCO membership is the main problem why many rural poor do not join RUSACCOs. Members participate in different aspects of the cooperatives, starting from attending general assembly up to board membership. They also participate actively in saving and borrowing activities of RUSACCO. The majority of the respondents believe the RUSACCO is a vital instrument in combating food insecurity. The empirical findings indicate that gender, marital status, occupation, educational level, participation in local leadership and participation in other income generation means determine the decision of rural poor to join a RUSACCO or not. The amount of saving is determined by household head occupation, farming experience and income level. While age of household head, primary occupation, farming experience, date of membership, annual total consumption expenditure, amount of saving and participation in other income generation activities influence members’ amount of borrowing by RUSACCO members. Finally, the study confirms that RUSACCO participation improves household food security. RUSACCO membership has made positive impact on household total consumption expenditure and food expenditure.

A microscopic study of structural and electronic properties of functionalized silicon surfaces based on first-principles

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future (opto-)electronic devices. Understanding the role played by the nature of the linking group and the chain length on the adsorption structures and electronic properties of these assemblies is vital to advance this technology. This Thesis is a study of such properties and contributes in particular to a microscopic understanding of induced changes in the work function of experimentally studied functionalized silicon surfaces. Using first-principles density functional theory (DFT), at the first step, we provide predictions for chemical trends in the work function of hydrogenated silicon (111) surfaces modified with various terminations. For nonpolar terminating atomic species such as F, Cl, Br, and I, the change in the work function is directly proportional to the amount of charge transferred from the surface, thus relating to the difference in electronegativity of the adsorbate and silicon atoms. The change is a monotonic function of coverage in this case, and the work function increases with increasing electronegativity. Polar species such as −TeH, −SeH, −SH, −OH, −NH2, −CH3, and −BH2 do not follow this trend due to the interaction of their dipole with the induced electric field at the surface. In this case, the magnitude and sign of the surface dipole moment need to be considered in addition to the bond dipole to generally describe the change in work function. Compared to hydrogenated surfaces, there is slight increase in the work function of H:Si(111)-XH, where X = Te, Se, and S, whereas reduction is observed for surfaces covered with −OH, −CH3, and −NH2. Next, we study the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si–(CH2)n–CH2 and H:Si–X–(CH2)n–CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)–Hexyl and (X)–Dodecyl functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0–3, n = 5–7, and n = 9–11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length. Later we continue by examining the work function tuning of H:Si(111) over a range of 1.73 eV through adsorption of alkyl monolayers with general formula -[Xhead-group]-(CnH2n)-[Xtail-group], X = O(H), S(H), NH(2). The work function is practically converged at 4 carbons (8 for oxygen), for head-group functionalization. For tail-group functionalization and with both head- and tail-groups, there is an odd-even effect in the behavior of the work function, with peak-to-peak amplitudes of up to 1.7 eV in the oscillations. This behavior is explained through the orientation of the terminal-group's dipole. The shift in the work function is largest for NH2-linked and smallest for SH-linked chains and is rationalized in terms of interface dipoles. Our study reveals that the choice of the head- and/or tail-groups effectively changes the impact of the alkyl chain length on the work function tuning using self-assembled monolayers and this is an important advance in utilizing hybrid functionalized Si surfaces. Bringing together the understanding gained from studying single type functionalization of H:Si(111) with different alkyl chains and bearing in mind how to utilize head-group, tail-group or both as well as monolayer coverage, in the final part of this Thesis we study functionalized H:Si(111) with binary SAMs. Aiming at enhancing work function adjustment together with SAM stability and coverage we choose a range of terminations and linker-chains denoted as –X–(Alkyl) with X = CH3, O(H), S(H), NH(2) and investigate the stability and work function of various binary components grafted onto H:Si(111) surface. Using binary functionalization with -[NH(2)/O(H)/S(H)]-[Hexyl/Dodecyl] we show that work function can be tuned within the interval of 3.65-4.94 eV and furthermore, enhance the SAM’s stability. Although direct Si-C grafted SAMs are less favourable compared to their counterparts with O, N or S linkage, regardless of the ratio, binary functionalized alkyl monolayers with X-alkyl (X = NH, O) is always more stable than single type alkyl functionalization with the same coverage. Our results indicate that it is possible to go beyond the optimum coverage of pure alkyl functionalized SAMs (50%) by adding a linker with the correct choice of the linker. This is very important since dense packed monolayers have fewer defects and deliver higher efficiency. Our results indicate that binary anchoring can modify the charge injection and therefore bond stability while preserving the interface electronic structure.