Large-scale structure of brown rat (Rattus norvegicus) populations in England: effects on rodenticide resistance

The brown rat (Rattus norvegicus) is a relatively recent (<300 years) addition to the British fauna, but by association with negative impacts on public health, animal health and agriculture, it is regarded as one of the most important vertebrate pest species. Anticoagulant rodenticides were introduced for brown rat control in the 1950s and are widely used for rat control in the UK, but long-standing resistance has been linked to control failures in some regions. One thus far ignored aspect of resistance biology is the population structure of the brown rat. This paper investigates the role population structure has on the development of anticoagulant resistance. Using mitochondrial and microsatellite DNA, we examined 186 individuals (from 15 counties in England and one location in Wales near the Wales–England border) to investigate the population structure of rural brown rat populations. We also examined individual rats for variations of the VKORC1 gene previously associated with resistance to anticoagulant rodenticides. We show that the populations were structured to some degree, but that this was only apparent in the microsatellite data and not the mtDNA data. We discuss various reasons why this is the case. We show that the population as a whole appears not to be at equilibrium. The relative lack of diversity in the mtDNA sequences examined can be explained by founder effects and a subsequent spatial expansion of a species introduced to the UK relatively recently. We found there was a geographical distribution of resistance mutations, and relatively low rate of gene flow between populations, which has implications for the development and management of anticoagulant resistance

Genetic factors regulating lung vasculature and immune cell functions associate with resistance to pneumococcal infection

Streptococcus pneumoniae is an important human pathogen responsible for high mortality and morbidity worldwide. The susceptibility to pneumococcal infections is controlled by as yet unknown genetic factors. To elucidate these factors could help to develop new medical treatments and tools to identify those most at risk. In recent years genome wide association studies (GWAS) in mice and humans have proved successful in identification of causal genes involved in many complex diseases for example diabetes, systemic lupus or cholesterol metabolism. In this study a GWAS approach was used to map genetic loci associated with susceptibility to pneumococcal infection in 26 inbred mouse strains. As a result four candidate QTLs were identified on chromosomes 7, 13, 18 and 19. Interestingly, the QTL on chromosome 7 was located within S. pneumoniae resistance QTL (Spir1) identified previously in a linkage study of BALB/cOlaHsd and CBA/CaOlaHsd F2 intercrosses. We showed that only a limited number of genes encoded within the QTLs carried phenotype-associated polymorphisms (22 genes out of several hundred located within the QTLs). These candidate genes are known to regulate TGFb signalling, smooth muscle and immune cells functions. Interestingly, our pulmonary histopathology and gene expression data demonstrated, lung vasculature plays an important role in resistance to pneumococcal infection. Therefore we concluded that the cumulative effect of these candidate genes on vasculature and immune cells functions as contributory factors in the observed differences in susceptibility to pneumococcal infection. We also propose that TGFbmediated regulation of fibroblast differentiation plays an important role in development of invasive pneumococcal disease.This work was supported by the European Union-funded Pneumopath Project HEALTH-F3-2009-222983. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer-reviewedPublisher Versio

Electronic Energy Transfer to the S2 Level of the Acceptor in Functionalised Boron Dipyrromethene Dyes

Taking the high road: Highly efficient electronic energy transfer takes place from a set of appended aryl polycyclic hydrocarbons to an expanded boron dipyrromethene (Bodipy)-based dye (see figure) despite negligible spectral overlap with the lowest-energy excited state localised on the acceptor.A multi-component array has been constructed around an expanded boron dipyrromethene (Bodipy) dye that absorbs and emits in the far-red region. One of the appendages is a perylene-based moiety that is connected to the boron atom of the terminal Bodipy by a 1,4-diethynylphenylene connector. Despite the fact that there is almost negligible spectral overlap between fluorescence from the perylene unit and absorption by the Bodipy residue, electronic energy transfer is rapid and essentially quantitative. It is concluded that at least half of the photons absorbed by perylene are transferred to the upper-lying singlet excited state (S2) associated with the Bodipy-based acceptor. The second appendage is a pyrene unit that is covalently linked to fluorene, through an ethynylene spacer, and to the boron atom of the Bodipy terminus, through a 1,4-diethynylphenylene connector. Pyrene absorbs and emits at higher energy than perylene and there is strong spectral overlap with the Bodipy-based S2 state, and none with the corresponding S1 state. Electronic energy transfer is now very fast and exclusively to the S2 state of the acceptor. It is difficult to compute reasonable estimates for the rates of Coulombic energy transfer, because of uncertainties in the orientation factor, but the principle mechanism is believed to arise from electron exchange. Comparison with an earlier array built around a conventional Bodipy dye indicates that there are comparable electronic coupling matrix elements for the two systems. It is notable that pyrene is more strongly coupled to the Bodipy unit than perylene in both arrays. These new arrays function as highly effective solar concentrators

The information system for LHC parameters and layouts

The construction of the Large Hadron Collider, LHC, at CERN implies both the handling of a huge amount of information and the control of the coherence of this information. The LHC machine parameters have to be maintained coherent as the design evolves from the conceptual stage to the actual, installed, machine and have to be made available to all concerned. Design data is provided in many different formats from the machine builders, drawings, technical documents, meeting notes, lattice simulation input files, etc. The World Wide Web is being used to make the information accessible both at CERN and at the external collaborating laboratories. In this paper we describe the implementation of an Oracle database as the central common repository for machine parameters and of information for the automatic generation of CAD layout drawings and WWW pages. This system is integrated in a larger context, the EDMS system for the LHC project, which encompasses both the accelerator and the experiments

Expression of RUNX1 correlates with poor patient prognosis in triple negative breast cancer

The RUNX1 transcription factor is widely recognised for its tumour suppressor effects in leukaemia. Recently a putative link to breast cancer has started to emerge, however the function of RUNX1 in breast cancer is still unknown. To investigate if RUNX1 expression was important to clinical outcome in primary breast tumours a tissue microarray (TMA) containing biopsies from 483 patients with primary operable invasive ductal breast cancer was stained by immunohistochemistry. RUNX1 was associated with progesterone receptor (PR)-positive tumours (P&#60;0.05), more tumour CD4+(P&#60;0.05) and CD8+(P&#60;0.01) T-lymphocytic infiltrate, increased tumour CD138+plasma cell (P&#60;0.01) and more CD68+macrophage infiltrate (P&#60;0.001). RUNX1 expression did not influence outcome of oestrogen receptor (ER)-positive or HER2-positive disease, however on univariate analysis a high RUNX1 protein was significantly associated with poorer cancer-specific survival in patients with ER-negative (P&#60;0.05) and with triple negative (TN) invasive breast cancer (P&#60;0.05). Furthermore, multivariate Cox regression analysis of cancer-specific survival showed a trend towards significance in ER-negative patients (P&#60;0.1) and was significant in triple negative patients (P&#60;0.05). Of relevance, triple negative breast cancer currently lacks good biomarkers and patients with this subtype do not benefit from the option of targeted therapy unlike patients with ER-positive or HER2-positive disease. Using multivariate analysis RUNX1 was identified as an independent prognostic marker in the triple negative subgroup. Overall, our study identifies RUNX1 as a new prognostic indicator correlating with poor prognosis specifically in the triple negative subtype of human breast cancer

‘I actually know that things will get better’:The many pathways to resilience of LGBTQIA+ youth in out-of-home care

Research on the lives of lesbian, gay, bisexual, transgender, queer, intersex, asexual and other forms of sexual identities and orientations (LGBTQIA+) youth in care has mainly examined their experiences from a risk-based approach, while few studies have explored their resilience experiences. Using in-depth interviews, the present study aims to illuminate the resilience experiences of 13 LGBTQIA+ young people in out-of-home care in the Netherlands. Four themes emerged from their narratives: relationships that support and empower; construction of a positive identity around their sexual orientation and gender identity and expression (SOGIE); community involvement and self-relying strategies. Our findings support the view of resilience as a complex process that shows at an individual, interpersonal and social level

Yours ever (well, maybe): Studies and signposts in letter writing

Electronic mail and other digital communications technologies seemingly threaten to end the era of handwritten and typed letters, now affectionately seen as part of snail mail. In this essay, I analyze a group of popular and scholarly studies about letter writing-including examples of pundits critiquing the use of e-mail, etiquette manuals advising why the handwritten letter still possesses value, historians and literary scholars studying the role of letters in the past and what it tells us about our present attitudes about digital communications technologies, and futurists predicting how we will function as personal archivists maintaining every document including e-mail. These are useful guideposts for archivists, providing both a sense of the present and the past in the role, value and nature of letters and their successors. They also provide insights into how such documents should be studied, expanding our gaze beyond the particular letters, to the tools used to create them and the traditions dictating their form and function. We also can discern a role for archivists, both for contributing to the literature about documents and in using these studies and commentaries, suggesting not a new disciplinary realm but opportunities for new interdisciplinary work. Examining a documentary form makes us more sensitive to both the innovations and traditions as it shifts from the analog to the digital; we can learn not to be caught up in hysteria or nostalgia about one form over another and archivists can learn about what they might expect in their labors to document society and its institutions. At one time, paper was part of an innovative technology, with roles very similar to the Internet and e-mail today. It may be that the shifts are far less revolutionary than is often assumed. Reading such works also suggests, finally, that archivists ought to rethink how they view their own knowledge and how it is constructed and used. © 2010 Springer Science+Business Media B.V

Poor survival outcomes in HER2 positive breast cancer patients with low grade, node negative tumours

We present a retrospective analysis on a cohort of low-grade, node-negative patients showing that human epidermal growth factor receptor 2 (HER2) status significantly affects the survival in this otherwise very good prognostic group. Our results provide support for the use of adjuvant trastuzumab in patients who are typically classified as having very good prognosis, not routinely offered standard chemotherapy, and who as such do not fit current UK prescribing guidelines for trastuzumab

Is the biology of breast cancer changing? A study of hormone receptor status 1984-1986 and 1996-1997

Using archived tumours, those from 1984-1986 and 1996-1997 underwent immunohistochemistry for hormone receptors and grade analysis. A significant shift towards more ER-positive and low-grade disease was found; this appears to reflect screening practices, but could still influence survival

DNA methylation is associated with codon degeneracy in a species of bumblebee

Social insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males, and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebee Bombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity, unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a targeted mutagen at these sites, providing substrate for selection via non-synonymous changes in the underlying genome. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.</p