Politics, Power, PISA: a genealogy of mathematics education policy at second level in Ireland at the beginning of the 21st century

This thesis traces a genealogy of the discourse of mathematics education reform in Ireland at the beginning of the twenty first century at a time when the hegemonic political discourse is that of neoliberalism. It draws on the work of Michel Foucault to identify the network of power relations involved in the development of a single case of curriculum reform – in this case Project Maths. It identifies the construction of an apparatus within the fields of politics, economics and education, the elements of which include institutions like the OECD and the Government, the bureaucracy, expert groups and special interest groups, the media, the school, the State, state assessment and international assessment. Five major themes in educational reform emerge from the analysis: the arrival of neoliberal governance in Ireland; the triumph of human capital theory as the hegemonic educational philosophy here; the dominant role of OECD/PISA and its values in the mathematics education discourse in Ireland; the fetishisation of western scientific knowledge and knowledge as commodity; and the formation of a new kind of subjectivity, namely the subjectivity of the young person as a form of human-capital-to-be. In particular, it provides a critical analysis of the influence of OECD/PISA on the development of mathematics education policy here – especially on Project Maths curriculum, assessment and pedagogy. It unpacks the arguments in favour of curriculum change and lays bare their ideological foundations. This discourse contextualises educational change as occurring within a rapidly changing economic environment where the concept of the State’s economic aspirations and developments in science, technology and communications are reshaping both the focus of business and the demands being put on education. Within this discourse, education is to be repurposed and its consequences measured against the paradigm of the Knowledge Economy – usually characterised as the inevitable or necessary future of a carefully defined present.

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.

Comparative genome analysis of human bifidobacteria with commercial potential

This thesis describes two newly sequenced B. longum subsp. longum genomes and subsequent comparative analysis with publicly available B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis genomes (Chapter 2). The acquired data revealed a closed pan-genome for this bifidobacterial species and furthermore facilitated the definition of the B. longum core genome. The comparative analysis also highlights differences in the potential metabolic abilities of all three sub-species. Interestingly, phylogenetic analysis of the B. longum core genome indicated the existence of a novel B. longum subspecies. Characterisation of restriction-modification systems from two B. longum subsp. longum strains is described in Chapter 3. These defence mechanisms limit the uptake of genetic material, which was successfully demonstrated for some of the identified systems. When these systems were by-passed by methylation of DNA prior to the transformation procedure, the resulting transformation efficiency of both B. longum subsp. longum strains was increased to a level that allowed for the generation of mutants via homologous recombination. Arabinoxylan metabolism by B. longum subsp. longum NCIMB 8809 was investigated in Chapter 4 of this thesis. Transcriptome analysis allowed the identification of a number of genes involved in the degradation, uptake and utilisation of arabinoxylan. Biochemical analysis revealed that three of the identified genes encode arabinofuranosidase activity. Phenotypic assessment of a number of insertion mutants in genes identified by the transcriptome analysis revealed the essential role of two of these enzymes in arabinoxylan metabolism, and a third enzyme in the metabolism of debranched arabinan. Furthermore, this investigation revealed that B. longum subsp. longum NCIMB 8809 does not completely degrade arabinoxylan, but utilises the arabinose substitutions only, while leaving the xylan backbone untouched.Finally, Chapter 5 outlines that B. longum subsp. longum NCIMB 8809 is capable of removing ferulic and p-coumaric acid substitutions that originate from arabinoxylan. Analysis of the genome sequence led to the identification of a candidate gene for this activity, which was subsequently cloned and expressed in E. coli. Biochemical analysis revealed that the enzyme, designated here as FaeA, is indeed capable of releasing both ferulic and p-coumaric acid from arabinoxylan. Furthermore, it is shown that a derivative of B. longum subsp. longum NCIMB 8809 carrying an insertion mutation in faeA had lost the ability to release ferulic and p-coumaric acid from arabinoxylan, and that growth of this mutant strain is negatively affected when cultivated on growth-limiting levels of arabinoxylan.

Genome-scale analyses of health-promoting bacteria: probiogenomics

The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics in the elucidation of the molecular basis of probiosis using the well-recognized model probiotic bacteria genera Bifidobacterium and Lactobacillus as examples.

The analytical approach of the European Court of Human Rights in surveillance cases—the implications, justifications, and future of the Court’s reasoning, with a focus on the legislative impact in Ireland

A notable feature of the surveillance case law of the European Court of Human Rights has been the tendency of the Court to focus on the “in accordance with the law” aspect of the Article 8 ECHR inquiry. This focus has been the subject of some criticism, but the impact of this approach on the manner in which domestic surveillance legislation has been formulated in the Party States has received little scholarly attention. This thesis addresses that gap in the literature through its consideration of the Interception of Postal Packets and Telecommunications Messages (Regulation) Act, 1993 and the Criminal Justice (Surveillance) Act, 2009. While both Acts provide several of the safeguards endorsed by the European Court of Human Rights, this thesis finds that they suffer from a number of crucial weaknesses that undermine the protection of privacy. This thesis demonstrates how the focus of the European Court of Human Rights on the “in accordance with the law” test has resulted in some positive legislative change. Notwithstanding this fact, it is maintained that the legality approach has gained prominence at the expense of a full consideration of the “necessary in a democratic society” inquiry. This has resulted in superficial legislative responses at the domestic level, including from the Irish government. Notably, through the examination of a number of more recent cases, this project discerns a significant alteration in the interpretive approach adopted by the European Court of Human Rights regarding the application of the necessity test. The implications of this development are considered and the outlook for Irish surveillance legislation is assessed.

The human impacts of flower farm development in the Ethiopian Rift Valley region

The flower industry has a reputation for heavy usage of toxic chemicals and polluting the environment, enormous consumption of water, and poor working condition and low wage level in various parts of the world. It is unfortunate that this industry is adamant to change and repeating the same mistakes in Ethiopia. Because of this, - there is a growing concern among the general public and the international community about sustainability of the Ethiopian flower industry. Consequently, working conditions in the flower industry, impacts of wage income on the livelihoods of employees, coping strategies of low wage flower farm workers, impacts of flower farms on the livelihoods of local people and environmental pollution and conflict, were analysed. Both qualitative and quantitative research methods were employed. Four quantitative data sets: labour practice, employees’ income and expenditure, displaced household, and flower grower views survey were collected between 2010 and 2012. Robust regression to identify the determinants of wage levels, and Multinomial logit to identify the determinants of coping strategies of flower farm workers and displaced households were employed. The findings show the working conditions in flower farms are characterized by low wages, job insecurity and frequent violation of employees’ rights, and poor safety measures. To ensure survival of their family, land dispossessed households adopt a wide range of strategies including reduction in food consumption, sharing oxen, renting land, share cropping, and shifting staple food crops. Most experienced scarcity of water resources, lack of grazing areas, death of herds and reduced numbers of livestock due to water source pollution. Despite the Ethiopian government investment in attracting and creating conducive environment for investors, not much was accomplished when it comes to enforcing labour laws and environmental policies. Flower farm expansion in Ethiopia, as it is now, can be viewed as part of the global land and water grab and is not all inclusive and sustainable. Several recommendations are made to improve working conditions, maximize the benefits of flower industry to the society, and to the country at large.

Identification of RNA editing in the human exome and development of DARNED DatabaseSF

RNA editing is a biological phenomena that alters nascent RNA transcripts by insertion, deletion and/or substitution of one or a few nucleotides. It is ubiquitous in all kingdoms of life and in viruses. The predominant editing event in organisms with a developed central nervous system is Adenosine to Inosine deamination. Inosine is recognized as Guanosine by the translational machinery and reverse-transcriptase. In primates, RNA editing occurs frequently in transcripts from repetitive regions of the genome. In humans, more than 500,000 editing instances have been identified, by applying computational pipelines on available ESTs and high-throughput sequencing data, and by using chemical methods. However, the functions of only a small number of cases have been studied thoroughly. RNA editing instances have been found to have roles in peptide variants synthesis by non-synonymous codon substitutions, transcript variants by alterations in splicing sites and gene silencing by miRNAs sequence modifications. We established the Database of RNA EDiting (DARNED) to accommo-date the reference genomic coordinates of substitution editing in human, mouse and fly transcripts from published literatures, with additional information on edited genomic coordinates collected from various databases e.g. UCSC, NCBI. DARNED contains mostly Adenosine to Inosine editing and allows searches based on genomic region, gene ID, and user provided sequence. The Database is accessible at http://darned.ucc.ie RNA editing instances in coding region are likely to result in recoding in protein synthesis. This encouraged me to focus my research on the occurrences of RNA editing specific CDS and non-Alu exonic regions. By applying various filters on discrepancies between available ESTs and their corresponding reference genomic sequences, putative RNA editing candidates were identified. High-throughput sequencing was used to validate these candidates. All predicted coordinates appeared to be either SNPs or unedited.