Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast]

On the structure of eigenfunctions corresponding to embedded eigenvalues of locally perturbed periodic graph operators

The article is devoted to the following question. Consider a periodic self-adjoint difference (differential) operator on a graph (quantum graph) G with a co-compact free action of the integer lattice Z^n. It is known that a local perturbation of the operator might embed an eigenvalue into the continuous spectrum (a feature uncommon for periodic elliptic operators of second order). In all known constructions of such examples, the corresponding eigenfunction is compactly supported. One wonders whether this must always be the case. The paper answers this question affirmatively. What is more surprising, one can estimate that the eigenmode must be localized not far away from the perturbation (in a neighborhood of the perturbation's support, the width of the neighborhood determined by the unperturbed operator only). The validity of this result requires the condition of irreducibility of the Fermi (Floquet) surface of the periodic operator, which is expected to be satisfied for instance for periodic Schroedinger operators.Comment: Submitted for publicatio

Policies for ecological intensification of crop production

Ecological intensification aims to increase crop productivity by enhancing biodiversity and associated ecosystem services, while minimizing the use of synthetic inputs and cropland expansion. Policies to promote ecological intensification have emerged in different countries, but they are still scarce and vary widely across regions. Here, we propose ten policy targets that governments can follow for ecological intensification

`In pursuit of the Nazi mind?' the deployment of psychoanalysis in the allied struggle against Germany

This paper discusses how psychoanalytic ideas were brought to bear in the Allied struggle against the Third Reich and explores some of the claims that were made about this endeavour. It shows how a variety of studies of Fascist psychopathology, centred on the concept of superego, were mobilized in military intelligence, post-war planning and policy recommendations for ‘denazification’. Freud's ideas were sometimes championed by particular army doctors and government planners; at other times they were combined with, or displaced by, competing, psychiatric and psychological forms of treatment and diverse studies of the Fascist ‘personality’. This is illustrated through a discussion of the treatment and interpretation of the deputy leader of the Nazi Party, Rudolf Hess, after his arrival in Britain in 1941

Capturing and testing perceptual-cognitive expertise: A comparison of stationary and movement response methods

Numerous methods have been used to study expertise and performance. In the present article, we compare the cognitive thought processes of skilled soccer players when responding to film-based simulations of defensive situations involving two different experimental conditions. Participants either remained stationary in a seated position (n = 10) or were allowed to move (n = 10) in response to life-size film sequences of 11 versus 11 open-play soccer situations viewed from a player’s perspective. Response accuracy and retrospective verbal reports of thinking were collected across the two task conditions. In the movement-based response group, participants generated a greater number of verbal report statements, including a higher proportion of evaluation, prediction, and action planning statements, than did participants in the stationary group. Findings suggest that the processing strategies employed during performance differ depending on the nature of the response required of participants. Implications for behavioral methods and experimental design are discussed

Nanocomposite Nafion-Silica membranes for direct methanol fuel cells

Commercially available proton exchange membranes such as Nafion do not meet the requirements for high power density direct methanol fuel cells, partly due to their high methanol permeability. The aim of this work is to develop a new class of high-proton conductivity membranes, with thermal and mechanical stability similar to Nafion and reduced methanol permeability. Nanocomposite membranes were produced by the in-situ sol-gel synthesis of silicon dioxide particles in preformed Nafion membranes. Microstructural modification of Nafion membranes with silica nanoparticles was shown in this work to reduce methanol crossover from 7.48x10-6 cm2s^-1 for pure Nafion® to 2.86 x10-6 cm2s^-1 for nanocomposite nafion membranes (Methanol 50% (v/v) solution, 75 degrees C). Best results were achieved with a silica composition of 2.6% (w/w). We propose that silica inhibits the conduction of methanol through Nafion by blocking sites necessary for methanol diffusion through the polymer electrolyte membrane. Effects of surface chemistry, nanoparticle formation and interactions with Nafion matrix are further addressed

Improving students’ ability at writing narrative text by using outline technique at the first grade of Mal Uin Su Medan in academic year 2016/2017

This research was aimed to know the students’ ability at writing narrative text by using outline technique. The research was conducted by using classroom action research. The subjects of this study were 36 of the tenth grade students of MAL UIN SU Medan in academic year 2016/2017. In doing this research, the technique of analyzing data was applied by using qualitative and quantitative approach. The qualitative data was taken from interview, observation, diary notes and documentation. The quantitative data was taken from the test. The result of the data analyzing showed that there was an improving on the students writing narrative text by using outline technique from each cycle. It was showed from mean of pre test was 51.41 and the mean of the students’ score for the post test I was 71.86, and the mean of the students’ score for post test II was 75.33. And based on interview, observation sheet, diary notes result and documentation showed that the students’ response at writing narrative text by using outline technique was good. It was found that teaching writing narrative text by using outline technique could improve the students’ ability

The use of electrochemical sensors for monitoring urban air quality in low-cost, high-density networks

Measurements at appropriate spatial and temporal scales are essential for understanding and monitoring spatially heterogeneous environments with complex and highly variable emission sources, such as in urban areas. However, the costs and complexity of conventional air quality measurement methods means that measurement networks are generally extremely sparse. In this paper we show that miniature, low-cost electrochemical gas sensors, traditionally used for sensing at parts-per-million (ppm) mixing ratios can, when suitably configured and operated, be used for parts-per-billion (ppb) level studies for gases relevant to urban air quality. Sensor nodes, in this case consisting of multiple individual electrochemical sensors, can be low-cost and highly portable, thus allowing the deployment of scalable high-density air quality sensor networks at fine spatial and temporal scales, and in both static and mobile configurations.This work was supported by EPSRC (grant number EP/E002102/1) and the Department for Transport

Mutations of the BRAF gene in human cancer

Cancers arise owing to the accumulation of mutations in critical genes that alter normal programmes of cell proliferation, differentiation and death. As the first stage of a systematic genome-wide screen for these genes, we have prioritized for analysis signalling pathways in which at least one gene is mutated in human cancer. The RAS RAF MEK ERK MAP kinase pathway mediates cellular responses to growth signals. RAS is mutated to an oncogenic form in about 15% of human cancer. The three RAF genes code for cytoplasmic serine/threonine kinases that are regulated by binding RAS. Here we report BRAF somatic missense mutations in 66% of malignant melanomas and at lower frequency in a wide range of human cancers. All mutations are within the kinase domain, with a single substitution (V599E) accounting for 80%. Mutated BRAF proteins have elevated kinase activity and are transforming in NIH3T3 cells. Furthermore, RAS function is not required for the growth of cancer cell lines with the V599E mutation. As BRAF is a serine/threonine kinase that is commonly activated by somatic point mutation in human cancer, it may provide new therapeutic opportunities in malignant melanoma