Structure and function analysis of the poliovirus cis-acting replication element (CRE)

The poliovirus cis-acting replication element (CRE) templates the uridylylation of VPg, the protein primer for genome replication. The CRE is a highly conserved structural RNA element in the enteroviruses and located within the polyprotein-coding region of the genome. We have determined the native structure of the CRE, defined the regions of the structure critical for activity, and investigated the influence of genomic location on function. Our results demonstrate that a 14-nucleotide unpaired terminal loop, presented on a suitably stable stem, is all that is required for function. These conclusions complement the recent analysis of the 14-nucleotide terminal loop in the CRE of human rhinovirus type 14. The CRE can be translocated to the 5' noncoding region of the genome, at least 3.7-kb distant from the native location, without adversely influencing activity, and CRE duplications do not adversely influence replication. We do not have evidence for a specific interaction between the CRE and the RNA-binding 3CD(pro) complex, an essential component of the uridylylation reaction, and the mechanism by which the CRE is coordinated and orientated during the reaction remains unclear. These studies provide a detailed overview of the structural determinants required for CRE function, and will facilitate a better understanding of the requirements for picornavirus replication.

The relation between content and structure in language production: an analysis of speech errors in semantic dementia

In order to explore the impact of a degraded semantic system on the structure of language production, we analysed transcripts from autobiographical memory interviews to identify naturally-occurring speech errors by eight patients with semantic dementia (SD) and eight age-matched normal speakers. Relative to controls, patients were significantly more likely to (a) substitute and omit open class words, (b) substitute (but not omit) closed class words, (c) substitute incorrect complex morphological forms and (d) produce semantically and/or syntactically anomalous sentences. Phonological errors were scarce in both groups. The study confirms previous evidence of SD patients’ problems with open class content words which are replaced by higher frequency, less specific terms. It presents the first evidence that SD patients have problems with closed class items and make syntactic as well as semantic speech errors, although these grammatical abnormalities are mostly subtle rather than gross. The results can be explained by the semantic deficit which disrupts the representation of a pre-verbal message, lexical retrieval and the early stages of grammatical encoding.

Algorithmic statistical analysis of electrophysiological data for the investigation of structure-activity relationship in single neurons

We are developing computational tools supporting the detailed analysis of the dependence of neural electrophysiological response on dendritic morphology. We approach this problem by combining simulations of faithful models of neurons (experimental real life morphological data with known models of channel kinetics) with algorithmic extraction of morphological and physiological parameters and statistical analysis. In this paper, we present the novel method for an automatic recognition of spike trains in voltage traces, which eliminates the need for human intervention. This enables classification of waveforms with consistent criteria across all the analyzed traces and so it amounts to reduction of the noise in the data. This method allows for an automatic extraction of relevant physiological parameters necessary for further statistical analysis. In order to illustrate the usefulness of this procedure to analyze voltage traces, we characterized the influence of the somatic current injection level on several electrophysiological parameters in a set of modeled neurons. This application suggests that such an algorithmic processing of physiological data extracts parameters in a suitable form for further investigation of structure-activity relationship in single neurons.

On the F-word: a corpus-based analysis of the media representation of Feminism in British and German press discourse,1990-2009

Research in social psychology has shown that public attitudes towards feminism are mostly based on stereotypical views linking feminism with leftist politics and lesbian orientation. It is claimed that such attitudes are due to the negative and sexualised media construction of feminism. Studies concerned with the media representation of feminism seem to confirm this tendency. While most of this research provides significant insights into the representation of feminism, the findings are often based on a small sample of texts. Also, most of the research was conducted in an Anglo-American setting. This study attempts to address some of the shortcomings of previous work by examining the discourse of feminism in a large corpus of German and British newspaper data. It does so by employing the tools of Corpus Linguistics. By investigating the collocation profiles of the search term feminism, we provide evidence of salient discourse patterns surrounding feminism in two different cultural contexts.

Analysis and manipulation of the structure of odor plumes from a piezo-electric release system and measurements of upwind flight of male Almond Moths, Cadra cautella, to pheromone plumes

We investigated the plume structure of a piezo-electric sprayer system, set up to release ethanol in a wind tunnel, using a fast response mini-photoionizaton detector. We recorded the plume structure of four different piezo-sprayer configurations: the sprayer alone; with a 1.6-mm steel mesh shield; with a 3.2-mm steel mesh shield; and with a 5 cm circular upwind baffle. We measured a 12 × 12-mm core at the center of the plume, and both a horizontal and vertical cross-section of the plume, all at 100-, 200-, and 400-mm downwind of the odor source. Significant differences in plume structure were found among all configurations in terms of conditional relative mean concentration, intermittency, ratio of peak concentration to conditional mean concentration, and cross-sectional area of the plume. We then measured the flight responses of the almond moth, Cadra cautella, to odor plumes generated with the sprayer alone, and with the upwind baffle piezo-sprayer configuration, releasing a 13:1 ratio of (9Z,12E)-tetradecadienyl acetate and (Z)-9-tetradecenyl acetate diluted in ethanol at release rates of 1, 10, 100, and 1,000 pg/min. For each configuration, differences in pheromone release rate resulted in significant differences in the proportions of moths performing oriented flight and landing behaviors. Additionally, there were apparent differences in the moths’ behaviors between the two sprayer configurations, although this requires confirmation with further experiments. This study provides evidence that both pheromone concentration and plume structure affect moth orientation behavior and demonstrates that care is needed when setting up experiments that use a piezo-electric release system to ensure the optimal conditions for behavioral observations.

A rare structure at the syntax-discourse interface: heritage and Spanish-dominant native speakers weigh in

The present study examines knowledge of the discourse-appropriateness of Clitic Right Dislocation (CLRD) in a population of Heritage (HS) and Spanish-dominant Native Speakers in order to test the predictions of the Interface Hypothesis (IH; Sorace 2011). The IH predicts that speakers in language contact situations will experience difficulties with integrating information involving the interface of syntax and discourse modules. CLRD relates a dislocated constituent to a discourse antecedent, requiring integration of syntax and pragmatics. Results from an acceptability judgment task did not support the predictions of the IH. No statistical differences between the HSs’ performance and that of L1-dominant native speakers were evidenced when participants were presented with an offline task. Thus, our study did not find any evidence of “incomplete acquisition” (Montrul 2008) as it pertains to this specific linguistic structure.

Modelling spectral reflectance of open cork oak woodland: a simulation analysis of the effects of vegetation structure and background

This study analyses the influence of vegetation structure (i.e. leaf area index and canopy cover) and seasonal background changes on moderate-resolution imaging spectrometer (MODIS)-simulated reflectance data in open woodland. Approximately monthly spectral reflectance and transmittance field measurements (May 2011 to October 2013) of cork oak tree leaves (Quercus suber) and of the herbaceous understorey were recorded in the region of Ribatejo, Portugal. The geometric-optical and radiative transfer (GORT) model was used to simulate MODIS response (red, near-infrared) and to calculate vegetation indices, investigating their response to changes in the structure of the overstorey vegetation and to seasonal changes in the understorey using scenarios corresponding to contrasting phenological status (dry season vs. wet season). The performance of normalized difference vegetation index (NDVI), soil-adjusted vegetation index (SAVI), and enhanced vegetation index (EVI) is discussed. Results showed that SAVI and EVI were very sensitive to the emergence of background vegetation in the wet season compared to NDVI and that shading effects lead to an opposing trend in the vegetation indices. The information provided by this research can be useful to improve our understanding of the temporal dynamic of vegetation, monitored by vegetation indices.

Discourse in Action: Introducing Mediated Discourse Analysis

From emails relating to adoption over the Internet to discussions in the airline cockpit, the spoken or written texts we produce can have significant social consequences. The area of Mediated Discourse Analysis considers texts in their social and cultural contexts to explore the actions individuals take with texts - and the consequences of those actions. Discourse in Action: brings together leading scholars from around the world in the area of Mediated Discourse Analysis reveals ways in which its theory and methodology can be used in research into contemporary social situations explores real situations and draws on real data in each chapter shows how analysis of texts in their social contexts broadens our understanding of the real world. Taken together, the chapters provide a comprehensive overview to the field and present a range of current studies that address some of the most important questions facing students and researchers in linguistics, education, communication studies and other fields.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Abstract Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North+East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST=0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST=0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and sub-group levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.