Trait directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass Holcus lanatus

The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate toler- ance in wild grass Holcus lanatus genotypes screened from the same habitat.

De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide poly- morphism (SNP) calling were conducted on RNA extracted from H.lanatus. Roche 454 sequencing data were assembled into c. 22 000 isotigs, and paired-end Illumina reads for phosphorus-starved (P) and phosphorus-treated (P+) genovars of tolerant (T) and nontoler- ant (N) phenotypes were mapped to this reference transcriptome.

Heatmaps of the gene expression data showed strong clustering of each P+/P treated genovar, as well as clustering by N/T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and P treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNA- binding protein and transposable elements.

A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP pro- files, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se.

Predator cue studies reveal strong trait-mediated effects in communities despite variation in experimental designs

Nonconsumptive or trait-mediated effects of predators on their prey often outweigh density-mediated interactions where predators consume prey. For instance, predator presence can alter prey behaviour, physiology, morphology and/or development. Despite a burgeoning literature, our ability to identify general patterns in prey behavioural responses may be influenced by the inconsistent methodologies of predator cue experiments used to assess trait-mediated effects. We therefore conducted a meta-analysis to highlight variables (e.g. water type, predator husbandry, exposure time) that may influence invertebrate prey's behavioural responses to fish predator cues. This revealed that changes in prey activity and refuge use were remarkably consistent overall, despite wide differences in experimental methodologies. Our meta-analysis shows that invertebrates altered their behaviour to predator cues of both fish that were fed the focal invertebrate and those that were fed other prey types, which suggests that invertebrates were not responding to specific diet information in the fish cues. Invertebrates also altered their behaviour regardless of predator cue addition regimes and fish satiation levels. Cue intensity and exposure time did not have significant effects on invertebrate behaviour. We also highlight that potentially confounding factors, such as parasitism, were rarely recorded in sufficient detail to assess the magnitude of their effects. By examining the likelihood of detecting trait-mediated effects under large variations in experimental design, our study demonstrates that trait-mediated effects are likely to have pervasive and powerful influences in nature.

Devoir de mémoire contre droit à l'imagination?:La querelle des historiens et des romanciers et la Seconde Guerre mondiale

conference paper given in Maynooth (History conference 18th 20th October 2013)

La présence ambiguë du "bon Allemand" dans le roman français de l’immédiat après-Seconde Guerre mondiale: Gary, Bory, Curtis

French Seminar Series
Belfast, December 2010

Identification of quantitative trait loci for rice grain element composition on an arsenic impacted soil:Influence of flowering time on genetic loci

Elements in grain crops such as iron, zinc and selenium are essential in the human diet, whereas elements such as arsenic are potentially toxic to humans. This study aims to identify quantitative trait loci (QTLs) for trace elements in rice grain. A field experiment was conducted in an arsenic enriched field site in Qiyang, China using the Bala x Azucena mapping population grown under standard field conditions. Grains were subjected to elemental analysis by inductively coupled plasma mass spectroscopy. QTLs were detected for the elemental composition within the rice grains, including for iron and selenium, which have previously been detected in this population grown at another location, indicating the stability of these QTLs. A correlation was observed between flowering time and a number of the element concentrations in grains, which was also revealed as co-localisation between flowering time QTLs and grain element QTLs. Unravelling the environmental conditions that influence the grain ionome appears to be complex, but from the results in this study one of the major factors which controls the accumulation of elements within the grain is flowering time.

Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.

Trait-Mediated Effects of Parasites on Invader-Native Interactions.

Parasites have a variety of behavioural effects on their hosts, which can in turn affect species with which the host interacts. Here we review how these trait-mediated indirect effects of parasites can alter the outcomes of invader-native interactions, illustrating with examples from the literature and with particular regard to the invader-native crustacean systems studied in our laboratories. Parasites may potentially inhibit or exacerbate invasions via their effects on host behaviour, in addition to their direct virulence effects on hosts. In several crustacean systems, we have found that parasites influence both host predation rates on intra- and inter-guild prey and host vulnerability to being preyed upon. These trait effects can theoretically alter invasion impact and patterns of coexistence, as they indirectly affect interactions between predators and prey with the potential for further ramifications to other species in the food web. The fitness consequences of parasite-induced trait-mediated effects are rarely considered in traditional parasitological contexts, but demand attention in the context of ecological communities. We can regard these trait effects as a form of cryptic virulence that only becomes apparent when hosts are examined in the context of the other species with which they interact.

Guerre et exil chez Louis-Ferdinand Céline

O nosso estudo incide, primordialmente, sobre as polémicas de carácter político e consequentes acusações de que Louis-Ferdinand Céline foi – e continua a ser – alvo. Tais aspectos conduzem-nos a questionar, com alguma veemência e perplexidade, as razões da sua fuga através da Alemanha, bem como as relações que estabeleceu com os Nazis durante a segunda guerra mundial. Num primeiro momento, elaborámos uma contextualização de cariz temporal e factual, tentando perceber – quiçá explicar -, o sentido das posições assumidas por Céline aquando da composição dos seus pamphlets, marcada por uma reivindicação violenta do seu antisemitismo e que surge, omnipresente, sob forma de cartas, entrevistas e outros escritos. Contudo, a essência do nosso trabalho consistiu numa análise detalhada das diferentes etapas dos anos de exílio do escritor, primeiro numa Alemanha devastada pela guerra, onde se refugia a partir de 17 de Junho de 1944 e mais tarde, na Dinamarca (1945-1951), de onde terá de responder às acusações de traição que lhe são dirigidas pela justiça francesa, antes de um regresso sem glória, a França, e de uma reabilitação tardia e titubeante. Os escritos que constituem o corpus do nosso trabalho traduzem, de modo inequívoco, a experiência amarga e cruel dos anos de exílio e da lembrança feita de dor e ódio, que o escritor sentiu profundamente, como um espinho na própria carne. Apesar do caminho tortuoso, que lhe confere uma aura de escritor “maldito”, Céline permanece, ainda hoje, como um dos maiores génios da literatura francesa do século XX.

Quel destin pour l'imaginaire épique et le héros guerrier dans l'écriture? Le témoignage de guerre au Québec de 1914 à nos jours

Cette thèse de doctorat, intitulée «Le récit personnel de guerre dans le Canada français/Québec du XXe siècle», est consacrée à l'étude du traitement de l'imaginaire épique et du héros guerrier dans plus d'une trentaine de témoignages de guerre d'expression française de 1914 à nos jours. Elle établit que le discours sur les combats qui s'y formule «retrouve spontanément le ton de l'épopée, langue maternelle du récit militaire héroïque, celle de l'Iliade » (Maurice RIEUNEAU, Guerre et révolution dans le roman français 1919-1939, Klincksieck, «Bibliothèque du XXe siècle», 1974, p. 157). Cette résilience épique et héroïque remarquable vaut pour toutes les époques. Fait à noter: même dans les récits contestataires, la contestation s'énonce en termes épiques, de héros qui poursuit son combat dans l'espace textuel. Voilà qui nuance quelque peu les résultats d'autres analyses, en particulier en Europe, où les spécialistes retiennent du XXe siècle: «Le récit de guerre [...] a périmé les plaisirs de l'épopée [...].» (Jean KAEMPFER, Poétique du récit de guerre, Paris, José Corti, 1998, p. 39). Avec la (post)modernité, l'épopée se réoriente. Dépassant le complexe du perdant qui marque plusieurs générations de francophones et les rend réceptifs aux valeurs de force et de virilité, le discours sort du repli sur soi, de l'isolement, de la solitude agressive pour pactiser avec l'ennemi juré (l'Allemand, le Japonais, mais aussi le Britannique, le Canadien anglais). Bref, l'identité, ébranlée par la différence, s'équilibre dans une démarche d'assainissement de la mémoire. L'affirmation progressive de soi se double d'une ouverture sur l'étranger, celui d'ailleurs et, à plus forte raison, d'ici.

Mon élève a le cancer--comment intervenir? perceptions d'enseignantes du primaire ayant accueilli un élève traité pour un cancer sur les services offerts et souhaités

Cette recherche aborde un phénomène encore peu documenté soit l'expérience d'enseignantes ayant accueilli un élève traité pour un cancer. Les études démontrent que l'école est peu préparée pour répondre aux besoins de ces élèves et offrir un soutien adéquat quant aux difficultés scolaires qu'ils risquent de présenter : fatigue, problème de mémoire, difficultés de concentration et d'apprentissage, etc. Résultant d'entrevues auprès de dix enseignantes, notre analyse qualitative a permis de dégager les services offerts et souhaités pour soutenir efficacement un élève traité pour un cancer dans son cheminement scolaire. En fonction de la situation et des difficultés de l'élève, les enseignantes disent avoir soutenu l'élève sur le plan affectif et social. Plusieurs proposent des moyens pour améliorer l'organisation de la classe. Enfin, notre discussion présente des pistes d'actions pour pallier l'absence de formation, accroître la concertation entre les milieux scolaires, communautaires et hospitaliers et favoriser l'inclusion scolaire de ces élèves.

Post awakening salivary cortisol secretion and trait well-being: The importance of sample timing accuracy

Indices of post awakening cortisol secretion (PACS), include the rise in cortisol(cortisol awakening response: CAR) and overall cortisol concentrations (e.g. area under the curve with reference to ground: AUCg) in the first 30—45 min. Both are commonly investigated in relation to psychosocial variables. Although sampling within the domestic setting is ecologically valid, participant non-adherence to the required timing protocol results in erroneous measurement of PACS and this may explain discrepancies in the literature linking these measures to trait well-being (TWB). We have previously shown that delays of little over 5 min(between awakening and the start of sampling) to result in erroneous CAR estimates. In this study, we report for the first time on the negative impact of sample timing inaccuracy (verified by electronic-monitoring) on the efficacy to detect significant relationships between PACS and TWB when measured in the domestic setting.Healthy females (N = 49, 20.5 ± 2.8 years) selected for differences in TWB collected saliva samples (S1—4) on 4 days at 0, 15, 30, 45 min post awakening, to determine PACS. Adherence to the sampling protocol was objectively monitored using a combination of electronic estimates of awakening (actigraphy) and sampling times (track caps).Relationships between PACS and TWB were found to depend on sample timing accuracy. Lower TWB was associated with higher post awakening cortisol AUCg in proportion to the mean sample timing accuracy (p < .005). There was no association between TWB and the CAR even taking into account sample timing accuracy. These results highlight the importance of careful electronic monitoring of participant adherence for measurement of PACS in the domestic setting. Mean sample timing inaccuracy, mainly associated with delays of >5 min between awakening and collection of sample 1 (median = 8 min delay), negatively impacts on the sensitivity of analysis to detect associations between PACS and TWB.

Chromosomal structure: a selectable trait for evolution

Dissertation presented to obtain the Ph.D degree in Evolutionary Biology