Taking advantage of an old concept, "illegitimate transcription", for a proposed novel method of genetic diagnosis of McArdle disease

McArdle disease is a metabolic disorder caused by pathogenic mutations in the PYGM gene. Timely diagnosis can sometimes be difficult with direct genomic analysis, which requires additional studies of cDNA from muscle transcripts. Although the "nonsense-mediated mRNA decay" (NMD) eliminates tissue-specific aberrant transcripts, there is some residual transcription of tissue-specific genes in virtually all cells, such as peripheral blood mononuclear cells (PBMCs).We studied a subset of the main types of PYGM mutations (deletions, missense, nonsense, silent, or splicing mutations) in cDNA from easily accessible cells (PBMCs) in 12 McArdle patients.Analysis of cDNA from PBMCs allowed detection of all mutations. Importantly, the effects of mutations with unknown pathogenicity (silent and splicing mutations) were characterized in PBMCs. Because the NMD mechanism does not seem to operate in nonspecific cells, PBMCs were more suitable than muscle biopsies for detecting the pathogenicity of some PYGM mutations, notably the silent mutation c.645G>A (p.K215=), whose effect in the splicing of intron 6 was unnoticed in previous muscle transcriptomic studies.We propose considering the use of PBMCs for detecting mutations that are thought to cause McArdle disease, particularly for studying their actual pathogenicity.

Iraq and world order: a Turkish perspective

G?l, Ayla. 'Iraq and world order: a Turkish perspective', in: 'The Iraq Crisis and World Order: Structural, Institutional and Normative Challenges', (Eds) Thakur, R., Sidhu, W. P. S., United Nations University Press, Hong Kong , pp.114-133, 2006 RAE2008

Audiences and Receptions of Sexual Violence in Contemporary Cinema

Barkre, M.; Mathijs, E.; Sexton, J.; Egan, K.; Hunter, R. and Selfe, M. (2007). Audiences and Receptions of Sexual Violence in Contemporary Cinema. London: British Board of Film Classification. RAE2008

Thomas Griffin of Corca Dhuibhne (1829-96) and the Irish Community of Lawrence, Massachusetts

RAE2008

Letter to nephew, 02/06/1868

Letter from Daniel Whedon to nephew, Daniel Avery Whedon. Dated February, 6, 1868.

Litigation-Generated Science: Why Should We Care?

BACKGROUND: In a 1994 Ninth Circuit decision on the remand of Daubert v. Merrell Dow Pharmaceuticals, Inc., Judge Alex Kosinski wrote that science done for the purpose of litigation should be subject to more stringent standards of admissibility than other science. OBJECTIVES: We analyze this proposition by considering litigation-generated science as a subset of science involving conflict of interest. DISCUSSION: Judge Kosinski's formulation suggests there may be reasons to treat science involving conflict of interest differently but raises questions about whether litigation-generated science should be singled out. In particular we discuss the similar problems raised by strategically motivated science done in anticipation of possible future litigation or otherwise designed to benefit the sponsor and ask what special treatment, if any, should be given to science undertaken to support existing or potential future litigation. CONCLUSION: The problems with litigation-generated science are not special. On the contrary, they are very general and apply to much or most science that is relevant and reliable in the courtroom setting.

Planning the deployment of fault-tolerant wireless sensor networks

Since Wireless Sensor Networks (WSNs) are subject to failures, fault-tolerance becomes an important requirement for many WSN applications. Fault-tolerance can be enabled in different areas of WSN design and operation, including the Medium Access Control (MAC) layer and the initial topology design. To be robust to failures, a MAC protocol must be able to adapt to traffic fluctuations and topology dynamics. We design ER-MAC that can switch from energy-efficient operation in normal monitoring to reliable and fast delivery for emergency monitoring, and vice versa. It also can prioritise high priority packets and guarantee fair packet deliveries from all sensor nodes. Topology design supports fault-tolerance by ensuring that there are alternative acceptable routes to data sinks when failures occur. We provide solutions for four topology planning problems: Additional Relay Placement (ARP), Additional Backup Placement (ABP), Multiple Sink Placement (MSP), and Multiple Sink and Relay Placement (MSRP). Our solutions use a local search technique based on Greedy Randomized Adaptive Search Procedures (GRASP). GRASP-ARP deploys relays for (k,l)-sink-connectivity, where each sensor node must have k vertex-disjoint paths of length ≤ l. To count how many disjoint paths a node has, we propose Counting-Paths. GRASP-ABP deploys fewer relays than GRASP-ARP by focusing only on the most important nodes – those whose failure has the worst effect. To identify such nodes, we define Length-constrained Connectivity and Rerouting Centrality (l-CRC). Greedy-MSP and GRASP-MSP place minimal cost sinks to ensure that each sensor node in the network is double-covered, i.e. has two length-bounded paths to two sinks. Greedy-MSRP and GRASP-MSRP deploy sinks and relays with minimal cost to make the network double-covered and non-critical, i.e. all sensor nodes must have length-bounded alternative paths to sinks when an arbitrary sensor node fails. We then evaluate the fault-tolerance of each topology in data gathering simulations using ER-MAC.

Not thinking straight? A critical discourse analysis of the 2006 Irish High Court ruling in Zappone and Gilligan v. Revenue Commissioners and Attorney General

The recognition and protection of constitutional rights is a fundamental precept. In Ireland, the right to marry is provided for in the equality provisions of Article 40 of the Irish Constitution (1937). However, lesbians and gay men are denied the right to marry in Ireland. The ‘last word’ on this issue came into being in the High Court in 2006, when Katherine Zappone and Ann Louise Gilligan sought, but failed, to have their Canadian marriage recognised in Ireland. My thesis centres on this constitutional court ruling. So as to contextualise the pursuit of marriage equality in Ireland, I provide details of the Irish trajectory vis-à-vis relationship and family recognition for same-sex couples. In Chapter One, I discuss the methodological orientation of my research, which derives from a critical perspective. Chapter Two denotes my theorisation of the principle of equality and the concept of difference. In Chapter Three, I discuss the history of the institution of marriage in the West with its legislative underpinning. Marriage also has a constitutional underpinning in Ireland, which derives from Article 41 of our Constitution. In Chapter Four, I discuss ways in which marriage and family were conceptualised in Ireland, by looking at historical controversies surrounding the legalisation of contraception and divorce. Chapter Five denotes a Critical Discourse Analysis of the High Court ruling in Zappone and Gilligan. In Chapter Six, I critique text from three genres of discourse, i.e. ‘Letters to the Editor’ regarding same-sex marriage in Ireland, communication from legislators vis-à-vis the 2004 legislative impediment to same-sex marriage in Ireland, and parliamentary debates surrounding the 2010 enactment of civil partnership legislation in Ireland. I conclude my research by reflecting on my methodological and theoretical considerations with a view to answering my research questions. Author’s Update: Following the outcome of the 2015 constitutional referendum vis-à-vis Article 41, marriage equality has been realised in Ireland.

Functional genomics of motile commensal intestinal bacteria

Flagella confer upon bacteria the ability to move and are therefore organelles of significant bacteriological importance. The innate immune system has evolved to recognise flagellin, (the major protein component of the bacterial flagellar filament). Flagellate microbes can potentially stimulate the immune systems of mammals, and thus have significant immunomodulatory potential. The flagellum-biogenesis genotype and phenotype of Lactobacillus ruminis, an autochthonous intestinal commensal, was studied. The flagellum-biogenesis genotypes of motile enteric Eubacterium and Roseburia species were also investigated. Flagellin proteins were recovered from these commensal species, their amino-termini were sequenced and the proteins were found to be pro-inflammatory, as assessed by measurement of interleukin-8 (IL-8) secretion from human intestinal epithelial cell lines. For L. ruminis, this IL-8 secretion required signalling through Toll Like Receptor 5. A model for the regulation of flagellum-biogenesis in L. ruminis was inferred from transcriptomics data and bioinformatics analyses. Motility gene expression in this species may be under the control of a novel regulator, LRC_15730. Potential promoters for genes encoding flagellin proteins in the Eubacterium and Roseburia genomes analysed were inferred in silico. Relative abundances of the target Eubacterium and Roseburia species in the intestinal microbiota of 25 elderly individuals were determined. These species were found to be variably abundant in these individuals. Motility genes from these species were variably detected in the shotgun metagenome databases generated by the ELDERMET project. This suggested that a greater depth of sequencing, or improved evenness of sequencing, would be required to capture the full diversity of microbial functions for specific target or low abundance species in microbial communities by metagenomics. In summary, this thesis used a functional genomics approach to describe flagellum-mediated motility in selected Gram-positive commensal bacteria. The regulation of flagellum biosynthesis in these species, and the consequences of flagella expression from a host-interaction perspective were also considered.

A study of diet and health in the elderly; the gut microbiota as a source of bioactive agents

The global proportion of older persons is increasing rapidly. Diet and the intestinal microbiota independently and jointly contribute to health in the elderly. The habitual dietary patterns and functional microbiota components of elderly subjects were investigated in order to identify specific effector mechanisms. A study of the dietary intake of Irish community-dwelling elderly subjects showed that the consumption of foods high in fat and/or sugar was excessive, while consumption of dairy foods was inadequate. Elderly females typically had a more nutrient- dense diet than males and a considerable proportion of subjects, particularly males, had inadequate intakes of calcium, magnesium, vitamin D, folate, zinc and vitamin C. The association between dietary patterns, glycaemic index and cognitive function was also investigated. Elderly subjects consuming ‘prudent’ dietary patterns had better cognitive function compared to those consuming ‘Western’ dietary patterns. Furthermore, fully-adjusted regression models revealed that a high glycaemic diet was associated with poor cognitive function, demonstrating a new link between nutrition and cognition. An extensive screening study of the elderly faecal-derived microbiota was also undertaken to examine the prevalence of antimicrobial production by intestinal bacteria. A number of previously characterised bacteriocins were isolated (gassericin T, ABP-118, mutacin II, enterocin L-50 and enterocin P) in this study. Interestingly, a Lactobacillus crispatus strain was found to produce a potentially novel antimicrobial compound. Full genome sequencing of this strain revealed the presence of three loci which exhibited varying degrees of homology with the genes responsible for helveticin J production in Lb. helveticus. An additional study comparing the immunomodulatory capacity of ‘viable’ and ‘non-viable’ Bifidobacterium strains found that Bifidobacterium-fermented milks (BFMs) containing ‘non-viable’ cells could stimulate levels of IL-10 and TNF-α in a manner similar to those stimulated by BFMs containing ‘viable’ cells in vitro.

Manipulation of magnetic anisotropy in nanostructures

Of late, the magnetic properties of micro/nano-structures have attracted intense research interest both fundamentally and technologically particularly to address the question that how the manipulation in the different layers of nanostructures, geometry of a patterned structure can affect the overall magnetic properties, while generating novel applications such as in magnetic sensors, storage devices, integrated inductive components and spintronic devices. Depending on the applications, materials with high, medium or low magnetic anisotropy and their possible manipulation are required. The most dramatic manifestation in this respect is the chance to manipulate the magnetic anisotropy over the intrinsic preferential direction of the magnetization, which can open up more functionality particularly for device applications. Types of magnetic anisotropies of different nanostructured materials and their manipulation techniques are investigated in this work. Detail experimental methods for the quantitative determination of magnetic anisotropy in nanomodulated Ni45Fe55 thin film are studied. Magnetic field induced in-plane rotations within the nanomodulated Ni45Fe55 continuous films revealed various rotational symmetries of magnetic anisotropy due to dipolar interactions showing a crossover from lower to higher fold of symmetry as a function of modulation geometry. In a second approach, the control of exchange anisotropy at ferromagnetic (FM) – aniferomagnetic (AFM) interface in multifferoic nanocomposite materials, where two different phase/types of materials were simultaneously synthesized, was investigated. The third part of this work was to study the electroplated thin films of metal alloy nanocomposite for enhanced exchange anisotropy. In this work a unique observation of an anti-clock wise as well as a clock wise hysteresis loop formation in the Ni,Fe solid solution with very low coercivity and large positive exchange anisotropy/exchange bias have been investigated. Hence, controllable positive and negative exchange anisotropy has been observed for the first time which has high potential applications such as in MRAM devices.

Alpha-fetoprotein controls female fertility and prenatal development of the gonadotropin-releasing hormone pathway through an antiestrogenic action

It has been shown previously that female mice homozygous for an alpha-fetoprotein (AFP) null allele are sterile as a result of anovulation, probably due to a defect in the hypothalamic-pituitary axis. Here we show that these female mice exhibit specific anomalies in the expression of numerous genes in the pituitary, including genes involved in the gonadotropin-releasing hormone pathway, which are underexpressed. In the hypothalamus, the gonadotropin-releasing hormone gene, Gnrh1, was also found to be down-regulated. However, pituitary gene expression could be normalized and fertility could be rescued by blocking prenatal estrogen synthesis using an aromatase inhibitor. These results show that AFP protects the developing female brain from the adverse effects of prenatal estrogen exposure and clarify a long-running debate on the role of this fetal protein in brain sexual differentiation.

Distinct functions of POT1 at telomeres.

The mammalian protein POT1 binds to telomeric single-stranded DNA (ssDNA), protecting chromosome ends from being detected as sites of DNA damage. POT1 is composed of an N-terminal ssDNA-binding domain and a C-terminal protein interaction domain. With regard to the latter, POT1 heterodimerizes with the protein TPP1 to foster binding to telomeric ssDNA in vitro and binds the telomeric double-stranded-DNA-binding protein TRF2. We sought to determine which of these functions-ssDNA, TPP1, or TRF2 binding-was required to protect chromosome ends from being detected as DNA damage. Using separation-of-function POT1 mutants deficient in one of these three activities, we found that binding to TRF2 is dispensable for protecting telomeres but fosters robust loading of POT1 onto telomeric chromatin. Furthermore, we found that the telomeric ssDNA-binding activity and binding to TPP1 are required in cis for POT1 to protect telomeres. Mechanistically, binding of POT1 to telomeric ssDNA and association with TPP1 inhibit the localization of RPA, which can function as a DNA damage sensor, to telomeres.

Long- incubation time- interferon-gamma release assays in response to PPD-, ESAT-6- and/or CFP-10 for the diagnosis of Mycobacterium tuberculosis infection in children.

Background:Diagnosis of childhood active tuberculosis (aTB) or latent Mycobacterium tuberculosis (Mtb) infection (LTBI) remains a challenge, and replacement of tuberculin skin tests (TST) by commercialized interferon-gamma release assays (IGRA) is not currently recommended.Methods:266 children between 1 month and 15 years of age, 214 being at risk of recent Mtb infection and 51 being included as controls, were prospectively enrolled. According results of clinical evaluation, TST, chest X-Ray and microbiology, children were classified as non-infected, LTBI or aTB. Long-incubation time PPD-, ESAT-6-, and CFP-10-IGRA were performed and evaluated for their accuracy to correctly classify the children.Results:Whereas both TST and PPD-IGRA were suboptimal to detect aTB, combining CFP-10-IGRA with TST or with PPD-IGRA allowed us to detect all the children with aTB, with 96% specificity for children who were positive for CFP-10-IGRA. Moreover, combination of CFP-10- and PPD-IGRA also detected 96% of children classified as LTBI, but a strong IFN-γ response to CFP-10 (>500 pg/ml) was highly suggestive of aTB at least among children less than 3 years old.Conclusions:Long-incubation time CFP-10- and PPD-IGRA should help the clinicians to identify quickly aTB or LTBI in young children.