Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae).

Past climatic changes and especially the ice ages have had a great impact on both the distribution and the genetic composition of plant populations, but whether they promoted speciation is still controversial. The autopolyploid complex Biscutella laevigata is a classical example of polyploidy linked to glaciations and is an interesting model to explore migration and speciation driven by climate changes in a complex alpine landscape. Diploid taxa survived the last glacial maximum in several never-glaciated areas and autotetraploids are clearly dominant in the central parts of the Alps; however, previous range-wide studies failed to identify their diploid ancestor(s). This study highlights the phylogeographical relationships of maternal lineages in the Western Alps and investigates the polyploidy process using plastid DNA sequences (trnS-trnG and trnK-intron) combined with plastid DNA length polymorphism markers, which were transferable among Brassicaceae species. Twenty-one distinct plastid DNA haplotypes were distinguished in 67 populations densely sampled in the Western Alps and main lineages were identified by a median-joining network. The external Alps harboured high levels of genetic diversity, while the Central Alps contained only a subset of haplotypes due to postglacial recolonization. Several haplotypes were restricted to local peripheral refugia and evidence of in situ survival in central nunataks was detected by the presence of highly differentiated haplotypes swamped by frequent ones. As hierarchical genetic structure pointed to an independent evolution of the species in different biogeographical districts, and since tetraploids displayed haplotypes belonging to different lineages restricted to either the northern or the southern parts of the Alpine chain, polytopic autopolyploidy was also apparent in the Western Alps

NADP-malate dehydrogenase gene evolution in Andropogoneae (Poaceae): gene duplication followed by sub-functionalization

• Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C(4) plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C(3); Erhartoideae) and maize (C(4); Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C(4); Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C(4) isoform has evolved over a broader range of panicoid grasses. • Methods Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios.Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach. • Key Results Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II. • Conclusions It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C(4) isoform as previously suggested. Nevertheless, some C(4) species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C(4) photosynthesis but are not required in every case

Polarization-dependence of anomalous scattering in brominated DNA and RNA molecules, and importance of crystal orientation in single- and multiple-wavelength anomalous diffraction phasing

In this paper the anisotropy of anomalous scattering at the Br K-absorption edge in brominated nucleotides is investigated, and it is shown that this effect can give rise to a marked directional dependence of the anomalous signal strength in X-ray diffraction data. This implies that choosing the correct orientation for crystals of such molecules can be a crucial determinant of success or failure when using single- and multiple-wavelength anomalous diffraction (SAD or MAD) methods to solve their structure. In particular, polarized absorption spectra on an oriented crystal of a brominated DNA molecule were measured, and were used to determine the orientation that yields a maximum anomalous signal in the diffraction data. Out of several SAD data sets, only those collected at or near that optimal orientation allowed interpretable electron density maps to be obtained. The findings of this study have implications for instrumental choices in experimental stations at synchrotron beamlines, as well as for the development of data collection strategy programs

NADP-Malate Dehydrogenase Gene Evolution in Andropogoneae (Poaceae): Gene Duplication Followed by Sub-functionalization

• Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C4 plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C3; Erhartoideae) and maize (C4; Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C4; Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C4 isoform has evolved over a broader range of panicoid grasses. • Methods Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios.Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach. • Key Results Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II. • Conclusions It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C4 isoform as previously suggested. Nevertheless, some C4 species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C4 photosynthesis but are not required in every cas

Arguments using ontological and causal knowledge (FoIKS 2014)

International audienceWe explore an approach to reasoning about causes via argumentation. We consider a causal model for a physical system, and we look for arguments about facts. Some arguments are meant to provide explanations of facts whereas some challenge these explanations and so on. At the root of argumentation here, are causal links ({A_1, ... ,A_n} causes B) and also ontological links (c_1 is_a} c_2). We introduce here a logical approach which provides a candidate explanation ({A_1, ... ,A_n} explains {B_1, ... ,B_m}) by resorting to an underlying causal link substantiated with appropriate ontological links. Argumentation is then at work from these various explanation links. A case study is developed: a severe storm Xynthia that devastated a county in France in 2010, with an unaccountably high number of casualties

Les phénomènes de dépendance à l’environnement: réflexions sur l’autonomie humaine à partir de la clinique neurologique

Dans cet article, nous proposons d’analyser la perte d’autonomie caractérisée par les phénomènes de dépendance à l’environnement observés chez certains patients neurologiques présentant des lésions des lobes frontaux. Des propositions théoriques issues de la neuropsychologie cognitive et de la théorie de la médiation sont développées et confrontées. La démarche offre l’occasion, au plan théorique, de questionner la détérioration possible du système de la personne suite à des lésions cérébrales et, au plan méthodologique, d’interroger notre manière d’examiner ces patients en confrontant les modèles théoriques aux observations clinique

Electronic Footprints in the Sand: Technologies for Assisting Domestic Violence Survivors

With the rapid growth and spread of Internet-based social support systems, the impact that these systems can make to society – be it good or bad – has become more significant and can make a real difference to people’s lives. As such, various aspects of these systems need to be carefully investigated and analysed, including their security/privacy issues. In this paper, we present our work in designing and implementing various technological features that can be used to assist domestic violence survivors in obtaining help without leaving traces which might lead to further violence from their abuser. This case study serves as the core of our paper, in which we outline our approach, various de- sign considerations – including difficulties in keeping browsing history private, our currently implemented solutions (single use URL, targeted history sanitita- tion agent, and secret graphical gateway), as well as novel ideas for future work (including location-based service advertising and deployment in the wild)

Frontal Lobe Functions in Normal Aging: Metacognition, Autonomy, and Quality of Life

BACKGROUND: Starting from the "frontal lobe hypothesis of cognitive aging", we aim to study the metacognitive functions (deception, reciprocity, cognitive and affective theory of mind), autonomy and quality of life in normal aging. METHODS: Eighty healthy subjects (30 young adults [YA] aged 20-40, 30 old adults [OA] aged 65-79 and 20 very old adults [VOA] aged 80 and over) participated in our study. Standard and novel neuropsychological tasks have been used, assessing abilities to understand others\u27 mental and affective states, deceptive and cooperative situations. RESULTS: OA and VOA\u27s performances are significantly poorer than those of YA on first-/second-order false beliefs, deception, reciprocity and emotion recognition tasks. VOA have made more errors than other participants on control false beliefs, general cognition, and memory tasks. Normal aging seems also to be characterized by a reduction in processing speed. The level of instrumental activities of daily living decreases with aging. Theory of mind is associated with individual general cognitive state and executive functions, but not with OA and VOA\u27s levels of autonomy and quality of life. CONCLUSION: In this study, we have shown an age-related deterioration of metacognitive functions, which does not seem to be associated with old adults\u27 autonomy and satisfaction of life. A good level of mental activity could be necessary to maintain satisfactory interpersonal relationships

Theory of Mind and Empathy in Preclinical and Clinical Huntington's Disease

We investigated cognitive and affective Theory of Mind (ToM) and empathy in patients with premanifest and manifest Huntington\u27s disease (HD). The relation between ToM performance and executive skills was also examined. 16 preclinical and 23 clinical HD patients, and 39 healthy subjects divided in 2 control groups were given a French adaptation of the Yoni test (Shamay-Tsoory and Aharon-Peretz, 2007) that examines first and second-order cognitive and affective ToM processing in separate conditions with a physical control condition. Participants were also given questionnaires of empathy and cognitive tests which mainly assessed executive functions (inhibition and mental flexibility). Clinical HD patients made significantly more errors than their controls in the first-and second-order cognitive and affective ToM conditions of the Yoni task, but exhibited no empathy deficits. However, there was no evidence that ToM impairment was related to cognitive deficits in these patients. Preclinical HD patients were unimpaired in ToM tasks and empathy measures compared to their controls. Our results are consistent with the idea that impaired affective and cognitive mentalising emerges with the clinical manifestation of HD, but is not necessarily part of the preclinical stage. Furthermore, these impairments appear independent of executive dysfunction and empathy