Interactions of Bunyamwera Virus Nucleocapsid Protein and Encapsidation of Viral RNA

This project concerns the identification and characterisation of some of the molecular interactions of the Bunyamwera virus (BUN) nucleocapsid (N) protein, and attempts to construct a model for encapsidation of viral RNA by N. BUN is the prototype virus of the Bunyaviridae, a family of negative-strand viruses with tripartite genomes. All BUN genome and antigenome RNAs are encapsidated by N. This interaction was investigated in vitro by expressing His-tagged BUN N in bacteria, purifying it in its native form and developing binding assays to analyse its association with a short radiolabelled riboprobe consisting of the termini of the BUNS segment. N was demonstrated to bind the riboprobe by Northwestern, gel electrophoretic mobility shift (GEMSA) and filter-binding assays. The complexes were found to possess a similar level of resistance to digestion with ribonuclease as authentic nucleocapsids. Analysis by GEMSA was interpreted to indicate complete encapsidation of the riboprobe by N, with a number of discrete complexes presumed to be intermediates in the sequential encapsidation process apparent. Filter-binding assays were utilised to determine the binding kinetics. The resultant dissociation constant was similar to dissociation constants obtained for other negative-strand virus N-RNA interactions and implied that binding was strong. Supporting the latter observation was the ability of complexes to form over a wide range of ionic conditions. The binding kinetics also indicated that the binding of N to the riboprobe was co-operative, reinforced by the demonstration that the capacity of N to bind RNA was dependent on its concentration. The 5' terminus of each segment RNA had been implicated in encapsidation initiation, but no direct evidence had been produced. To investigate the presence of an encapsidation signal, competitive binding assays were set up with various RNA species. The 5' 32 terminal nucleotides of the BUN S segment were bound selectively, implicating this region in encapsidation initiation. In addition, N was capable of binding any RNA non-selectively and to a low degree, indicating the presence of two modes of binding. Predictions of the secondary structure of 5' terminal sequences revealed potential stem-loops containing a consensus sequence in the loop region that had previously been found to be essential for transcription of a recombinant BUN S segment in a minireplicon system. The stem-loop was suggested to constitute an encapsidation signal, supported by the inability of an RNA containing the same sequence but not predicted to form the stem-loop to be bound selectively. BUN mRNA is not normally encapsidated and possesses a capped, heterogeneous primer sequence on its 5' end. The predictions of secondary structure were extended to propose a mechanism of inhibition of encapsidation by the primer sequence, which, under certain circumstances, was suggested to be reversible when required. The information obtained on N-RNA interactions was used to propose a model for encapsidation in BUN. The co-operative nature of N-RNA binding suggested that multimerisation of N took place. This was investigated by expressing N as fusion proteins in the mammalian two- hybrid system, and a potential self-association was identified. This was supported by the co-immunoprecipitation of native N with His-tagged N in mammalian cells. However, neither the amino nor the carboxy half of N was found to be capable of interacting with His-tagged N exclusively. No evidence of an interaction between the viral polymerase, L, and N or between L and the non-structural viral protein NSs was obtained using the mammalian two-hybrid system, and NSs was not found to multimerise. However, a weak interaction between N and NSs was identified. The potential role of this interaction in the mechanisms of transcription inhibition or interferon antagonism ascribed to NSs is discussed

Mapping Children's Discussions of Evidence in Science to Assess Collaboration and Argumentation

The research reported in this paper concerns the development of children's skills of interpreting and evaluating evidence in science. Previous studies have shown that school teaching often places limited emphasis on the development of these skills, which are necessary for children to engage in scientific debate and decision-making. The research, undertaken in the UK, involved four collaborative decision-making activities to stimulate group discussion, each was carried out with five groups of four children (10-11 years old). The research shows how the children evaluated evidence for possible choices and judged whether their evidence was sufficient to support a particular conclusion or the rejection of alternative conclusions. A mapping technique was developed to analyse the discussions and identify different "levels" of argumentation. The authors conclude that suitable collaborative activities that focus on the discussion of evidence can be developed to exercise children's ability to argue effectively in making decisions

Two Bee-Pollinated Plant Species Show Higher Seed Production when Grown in Gardens Compared to Arable Farmland

Background Insect pollinator abundance, in particular that of bees, has been shown to be high where there is a super-abundance of floral resources; for example in association with mass-flowering crops and also in gardens where flowering plants are often densely planted. Since land management affects pollinator numbers, it is also likely to affect the resultant pollination of plants growing in these habitats. We hypothesised that the seed or fruit set of two plant species, typically pollinated by bumblebees and/or honeybees might respond in one of two ways: 1) pollination success could be reduced when growing in a floriferous environment, via competition for pollinators, or 2) pollination success could be enhanced because of increased pollinator abundance in the vicinity. Methodology/Principal Findings We compared the pollination success of experimental plants of Glechoma hederacea L. and Lotus corniculatus L. growing in gardens and arable farmland. On the farms, the plants were placed either next to a mass-flowering crop (oilseed rape, Brassica napus L. or field beans, Vicia faba L.) or next to a cereal crop (wheat, Triticum spp.). Seed set of G. hederacea and fruit set of L. corniculatus were significantly higher in gardens compared to arable farmland. There was no significant difference in pollination success of G. hederacea when grown next to different crops, but for L. corniculatus, fruit set was higher in the plants growing next to oilseed rape when the crop was in flower. Conclusions/Significance The results show that pollination services can limit fruit set of wild plants in arable farmland, but there is some evidence that the presence of a flowering crop can facilitate their pollination (depending on species and season). We have also demonstrated that gardens are not only beneficial to pollinators, but also to the process of pollination

Chaste: an open source C++ library for computational physiology and biology

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials

Chikungunya Virus and Central Nervous System Infections in Children, India

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus best known for causing fever, rash, arthralgia, and occasional neurologic disease. By using real-time reverse transcription–PCR, we detected CHIKV in plasma samples of 8 (14%) of 58 children with suspected central nervous system infection in Bellary, India. CHIKV was also detected in the cerebrospinal fluid of 3 children

Analytical validation of a standardised scoring protocol for Ki67 immunohistochemistry on breast cancer excision whole sections: an international multicentre collaboration

Aims The nuclear proliferation marker Ki67 assayed by immunohistochemistry has multiple potential uses in breast cancer, but an unacceptable level of interlaboratory variability has hampered its clinical utility. The International Ki67 in Breast Cancer Working Group has undertaken a systematic programme to determine whether Ki67 measurement can be analytically validated and standardised among laboratories. This study addresses whether acceptable scoring reproducibility can be achieved on excision whole sections. Methods and results Adjacent sections from 30 primary ER+ breast cancers were centrally stained for Ki67 and sections were circulated among 23 pathologists in 12 countries. All pathologists scored Ki67 by two methods: (i) global: four fields of 100 tumour cells each were selected to reflect observed heterogeneity in nuclear staining; (ii) hot-spot: the field with highest apparent Ki67 index was selected and up to 500 cells scored. The intraclass correlation coefficient (ICC) for the global method [confidence interval (CI) = 0.87; 95% CI = 0.799-0.93] marginally met the prespecified success criterion (lower 95% CI >= 0.8), while the ICC for the hot-spot method (0.83; 95% CI = 0.74-0.90) did not. Visually, interobserver concordance in location of selected hot-spots varies between cases. The median times for scoring were 9 and 6 min for global and hot-spot methods, respectively. Conclusions The global scoring method demonstrates adequate reproducibility to warrant next steps towards evaluation for technical and clinical validity in appropriate cohorts of cases. The time taken for scoring by either method is practical using counting software we are making publicly available. Establishment of external quality assessment schemes is likely to improve the reproducibility between laboratories further

Analytical validation of a standardized scoring protocol for Ki67: phase 3 of an international multicenter collaboration

Pathological analysis of the nuclear proliferation biomarker Ki67 has multiple potential roles in breast and other cancers. However, clinical utility of the immunohistochemical (IHC) assay for Ki67 immunohistochemistry has been hampered by unacceptable between-laboratory analytical variability. The International Ki67 Working Group has conducted a series of studies aiming to decrease this variability and improve the evaluation of Ki67. This study tries to assess whether acceptable performance can be achieved on prestained core-cut biopsies using a standardized scoring method. Sections from 30 primary ER+ breast cancer core biopsies were centrally stained for Ki67 and circulated among 22 laboratories in 11 countries. Each laboratory scored Ki67 using three methods: (1) global (4 fields of 100 cells each); (2) weighted global (same as global but weighted by estimated percentages of total area); and (3) hot-spot (single field of 500 cells). The intraclass correlation coefficient (ICC), a measure of interlaboratory agreement, for the unweighted global method (0.87; 95% credible interval (CI): 0.81–0.93) met the prespecified success criterion for scoring reproducibility, whereas that for the weighted global (0.87; 95% CI: 0.7999–0.93) and hot-spot methods (0.84; 95% CI: 0.77–0.92) marginally failed to do so. The unweighted global assessment of Ki67 IHC analysis on core biopsies met the prespecified criterion of success for scoring reproducibility. A few cases still showed large scoring discrepancies. Establishment of external quality assessment schemes is likely to improve the agreement between laboratories further. Additional evaluations are needed to assess staining variability and clinical validity in appropriate cohorts of samples

Quantitative Historical Change in Bumblebee (Bombus spp.) Assemblages of Red Clover Fields

Flower visiting insects provide a vitally important pollination service for many crops and wild plants. Recent decline of pollinating insects due to anthropogenic modification of habitats and climate, in particular from 1950's onwards, is a major and widespread concern. However, few studies document the extent of declines in species diversity, and no studies have previously quantified local abundance declines. We here make a quantitative assessment of recent historical changes in bumblebee assemblages by comparing contemporary and historical survey data. species observed in the 1930's, five species were not observed at present. The latter were all long-tongued, late-emerging species.Because bumblebees are important pollinators, historical changes in local bumblebee assemblages are expected to severely affect plant reproduction, in particular long-tubed species, which are pollinated by long-tongued bumblebees

(Re)theorising laddish masculinities in higher education

In the context of renewed debates and interest in this area, this paper reframes the theoretical agenda around laddish masculinities in UK higher education, and similar masculinities overseas. These can be contextualised within consumerist neoliberal rationalities, the neoconservative backlash against feminism and other social justice movements, and the postfeminist belief that women are winning the ‘battle of the sexes’. Contemporary discussions of ‘lad culture’ have rightly centred sexism and men¹s violence against women: however, we need a more intersectional analysis. In the UK a key intersecting category is social class, and there is evidence that while working class articulations of laddism proceed from being dominated within alienating education systems, middle class and elite versions are a reaction to feeling dominated due to a loss of gender, class and race privilege. These are important differences, and we need to know more about the conditions which shape and produce particular performances of laddism, in interaction with masculinities articulated by other social groups. It is perhaps unhelpful, therefore, to collapse these social positions and identities under the banner of ‘lad culture’, as has been done in the past

Seoul Virus Associated with Pet Rats, Scotland, UK, 2019.

We describe a case of hemorrhagic fever with renal syndrome caused by Seoul virus in a woman in Scotland, UK. Whole-genome sequencing showed the virus belonged to a lineage characterized by recent international expansion, probably driven by trade in pet rats