Ultracold, radiative charge transfer in hybrid Yb ion – Rb atom traps

Ultracold hybrid ion–atom traps offer the possibility of microscopic manipulation of quantum coherences in the gas using the ion as a probe. However, inelastic processes, particularly charge transfer can be a significant process of ion loss and has been measured experimentally for the ${\rm Y}{{{\rm b}}^{+}}$ ion immersed in a Rb vapour. We use first-principles quantum chemistry codes to obtain the potential energy curves and dipole moments for the lowest-lying energy states of this complex. Calculations for the radiative decay processes cross sections and rate coefficients are presented for the total decay processes; ${\rm Y}{{{\rm b}}^{+}}(6{\rm s}{{\;}^{2}}{\rm S})+{\rm Rb}(5{\rm s}{{\;}^{2}}{\rm S})\to {\rm Yb}(6{{{\rm s}}^{2}}{{\;}^{1}}{\rm S})+{\rm R}{{{\rm b}}^{+}}(4{{{\rm p}}^{6}}{{\;}^{1}}{\rm S})+h\nu $ and ${\rm Y}{{{\rm b}}^{+}}(6{\rm s}{{\;}^{2}}{\rm S})+{\rm Rb}(5{\rm s}{{\;}^{2}}{\rm S})\to {\rm YbR}{{{\rm b}}^{+}}({{X}^{1}}{{\Sigma }^{+}})+h\nu $. Comparing the semi-classical Langevin approximation with the quantum approach, we find it provides a very good estimate of the background at higher energies. The results demonstrate that radiative decay mechanisms are important over the energy and temperature region considered. In fact, the Langevin process of ion–atom collisions dominates cold ion–atom collisions. For spin-dependent processes [1] the anisotropic magnetic dipole–dipole interaction and the second-order spin–orbit coupling can play important roles, inducing coupling between the spin and the orbital motion. They measured the spin-relaxing collision rate to be approximately five orders of magnitude higher than the charge-exchange collision rate [1]. Regarding the measured radiative charge transfer collision rate, we find that our calculation is in very good agreement with experiment and with previous calculations. Nonetheless, we find no broad resonances features that might underly a strong isotope effect. In conclusion, we find, in agreement with previous theory that the isotope anomaly observed in experiment remains an open question.

Numerical modelling of low temperature laser produced magnesium plasma

The two-dimensional laser-plasma-interaction hydrodynamic code POLLUX has been used to simulate the ablation of a magnesium target by a 30-ns, 248-nm KrF excimer laser at low laser fluences of ≤10 J cm2. This code, originally written for much higher laser intensities, has been recently extended to include a detailed description of the equation of state in order to treat changes of phase within the target material, and also includes a Thomas Fermi description of the electrons. The simulated temporal and spatial evolution of the plasma plume in the early phase of the expansion (≤100 ns) is compared with experimental interferometric measurements of electron density. The expansion dynamics are in good agreement, although the simulated electron number density is about 2.5 times higher than the experimental values.

Mapping neutral, ion and electron number densities within laser ablated plasma plumes

Spatially and temporally varying neutral, ion and electron number densities have been mapped out within laser ablated plasma plumes expanding into vacuum. Ablation of a magnesium target was performed using a KrF laser, 30 ns pulse duration and 248 nm wavelength. During the initial stage of plasma expansion (t <EQ 100 ns) interferometry has been used to obtain line averaged electron number densities, for laser power densities on target in the range 1.3 - 3.0 X 108 W/cm2. Later in the plasma expansion (t equals 1 microsecond(s) ) simultaneous absorption and laser induced fluorescence spectroscopy has been used to determine 3D neutral and ion number densities, for a power density equal to 6.7 X 107 W/cm2. Two distinct regions within the plume were identified. One is a fast component (approximately 106 cm-1) consisting of ions and neutrals with maximum number densities observed to be approximately 30 and 4 X 1012 cm-3 respectively, and the second consists of slow moving neutral material at a number density of up to 1015 cm-3. Additionally a Langmuir probe has been used to obtain ion and electron number densities at very late times in the plasma expansion (1 microsecond(s) <EQ t <EQ 15 microsecond(s) ). A copper target was ablated using a Nd:YAG laser, 7.5 ns duration and 532 nm (2 (omega) ) wavelength, with a power density on target equal to 6 X 108 W/cm2. Two regions within the plume with different velocities were observed. Within a fast component (approximately 3 X 106 cms-1) electron and ion number densities of the order 5 X 1012 cm-3 were observed and within the second slower component (approximately 106 cms-1) electron and ion number densities of the order 1 - 2 X 1013 cm-3 were determined.

Turbulent amplification of magnetic fields in laboratory laser-produced shock waves

X-ray and radio observations of the supernova remnant Cassiopeia A reveal the presence of magnetic fields about 100 times stronger than those in the surrounding interstellar medium. Field coincident with the outer shock probably arises through a nonlinear feedback process involving cosmic rays. The origin of the large magnetic field in the interior of the remnant is less clear but it is presumably stretched and amplified by turbulent motions. Turbulence may be generated by hydrodynamic instability at the contact discontinuity between the supernova ejecta and the circumstellar gas9. However, optical observations of Cassiopeia A indicate that the ejecta are interacting with a highly inhomogeneous, dense circumstellar cloud bank formed before the supernova explosion. Here we investigate the possibility that turbulent amplification is induced when the outer shock overtakes dense clumps in the ambient medium. We report laboratory experiments that indicate the magnetic field is amplified when the shock interacts with a plastic grid. We show that our experimental results can explain the observed synchrotron emission in the interior of the remnant. The experiment also provides a laboratory example of magnetic field amplification by turbulence in plasmas, a physical process thought to occur in many astrophysical phenomena.

John Birks: Pioneer in quantitative palaeoecology

We describe the career of John Birks as a pioneering scientist who has, over a career spanning five decades, transformed palaeoecology from a largely descriptive to a rigorous quantitative science relevant to contemporary questions in ecology and environmental change. We review his influence on students and colleagues not only at Cambridge and Bergen Universities, his places of primary employment, but also on individuals and research groups in Europe and North America. We also introduce the collection of papers that we have assembled in his honour. The papers are written by his former students and close colleagues and span many of the areas of palaeoecology to which John himself has made major contributions. These include the relationship between ecology and palaeoecology, late-glacial and Holocene palaeoecology, ecological succession, climate change and vegetation history, the role of palaeoecological techniques in reconstructing and understanding the impact of human activity on terrestrial and freshwater ecosystems and numerical analysis of multivariate palaeoecological data.

Developed turbulence and nonlinear amplification of magnetic fields in laboratory and astrophysical plasmas

The visible matter in the universe is turbulent and magnetized. Turbulence in galaxy clusters is produced by mergers and by jets of the central galaxies and believed responsible for the amplification of magnetic fields. We report on experiments looking at the collision of two laser-produced plasma clouds, mimicking, in the laboratory, a cluster merger event. By measuring the spectrum of the density fluctuations, we infer developed, Kolmogorov-like turbulence. From spectral line broadening, we estimate a level of turbulence consistent with turbulent heating balancing radiative cooling, as it likely does in galaxy clusters. We show that the magnetic field is amplified by turbulent motions, reaching a nonlinear regime that is a precursor to turbulent dynamo. Thus, our experiment provides a promising platform for understanding the structure of turbulence and the amplification of magnetic fields in the universe.

The ETS family member GABPα modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer

In prostate cancer (PC), the androgen receptor (AR) is a key transcription factor at all disease stages, including the advanced stage of castrate-resistant prostate cancer (CRPC). In the present study, we show that GABPα, an ETS factor that is up-regulated in PC, is an AR-interacting transcription factor. Expression of GABPα enables PC cell lines to acquire some of the molecular and cellular characteristics of CRPC tissues as well as more aggressive growth phenotypes. GABPα has a transcriptional role that dissects the overlapping cistromes of the two most common ETS gene fusions in PC: overlapping significantly with ETV1 but not with ERG target genes. GABPα bound predominantly to gene promoters, regulated the expression of one-third of AR target genes and modulated sensitivity to AR antagonists in hormone responsive and castrate resistant PC models. This study supports a critical role for GABPα in CRPC and reveals potential targets for therapeutic intervention.

HES6 drives a critical AR transcriptional programme to induce castration-resistant prostate cancer through activation of an E2F1-mediated cell cycle network

Castrate-resistant prostate cancer (CRPC) is poorly characterized and heterogeneous and while the androgen receptor (AR) is of singular importance, other factors such as c-Myc and the E2F family also play a role in later stage disease. HES6 is a transcription co-factor associated with stem cell characteristics in neural tissue. Here we show that HES6 is up-regulated in aggressive human prostate cancer and drives castration-resistant tumour growth in the absence of ligand binding by enhancing the transcriptional activity of the AR, which is preferentially directed to a regulatory network enriched for transcription factors such as E2F1. In the clinical setting, we have uncovered a HES6-associated signature that predicts poor outcome in prostate cancer, which can be pharmacologically targeted by inhibition of PLK1 with restoration of sensitivity to castration. We have therefore shown for the first time the critical role of HES6 in the development of CRPC and identified its potential in patient-specific therapeutic strategies.

The androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man

The androgen receptor (AR) regulates prostate cell growth in man, and prostate cancer is the commonest cancer in men in the UK. We present a comprehensive analysis of AR binding sites in human prostate cancer tissues, including castrate-resistant prostate cancer (CRPC). We identified thousands of AR binding sites in CRPC tissue, most of which were not identified in PC cell lines. Many adjacent genes showed AR regulation in xenografts but not in cultured LNCaPs, demonstrating an in-vivo-restricted set of AR-regulated genes. Functional studies support a model of altered signaling in vivo that directs AR binding. We identified a 16 gene signature that outperformed a larger in-vitro-derived signature in clinical data sets, showing the importance of persistent AR signaling in CRPC.

Learning to be Boys: Reading the Lessons of Shakespeare’s Love’s Labour’s Lost and Marston’s What You Will

This essay focuses on the lessons of Love’s Labour’s Lost’s pageboy-schoolboy-boy actor, Moth, to examine the production of boyhood in early modern culture. It reads Shakespeare’s boy character alongside John Marston’s schoolboy, Holofernes Pippo, in What You Will to investigate the ways in which school lessons might be deployed to produce aged and gendered identities that complicate traditional understandings of early modern masculinity. Reading the comic staging of lessons in these plays, it will suggest that while the educational system aimed to produce gendered subjects, early modern masculine identities exist as a range of categories on a developmental scale. It will propose that although Moth and Pippo comically expose the limits of many pedagogical methods to produce ‘men’, they demonstrate the ways in which these characters learn to be boys. Finally, it will consider the extent to which this production of early modern age and gender identity in the plays is paralleled by the historical boy actors performing these roles.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.

METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.

FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.

INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer

The androgen receptor (AR) is the dominant growth factor in prostate cancer (PCa). Therefore, understanding how ARs regulate the human transcriptome is of paramount importance. The early effects of castration on human PCa have not previously been studied 27 patients medically castrated with degarelix 7 d before radical prostatectomy. We used mass spectrometry, immunohistochemistry, and gene expression array (validated by reverse transcription-polymerase chain reaction) to compare resected tumour with matched, controlled, untreated PCa tissue. All patients had levels of serum androgen, with reduced levels of intraprostatic androgen at prostatectomy. We observed differential expression of known androgen-regulated genes (TMPRSS2, KLK3, CAMKK2, FKBP5). We identified 749 genes downregulated and 908 genes upregulated following castration. AR regulation of α-methylacyl-CoA racemase expression and three other genes (FAM129A, RAB27A, and KIAA0101) was confirmed. Upregulation of oestrogen receptor 1 (ESR1) expression was observed in malignant epithelia and was associated with differential expression of ESR1-regulated genes and correlated with proliferation (Ki-67 expression).

PATIENT SUMMARY: This first-in-man study defines the rapid gene expression changes taking place in prostate cancer (PCa) following castration. Expression levels of the genes that the androgen receptor regulates are predictive of treatment outcome. Upregulation of oestrogen receptor 1 is a mechanism by which PCa cells may survive despite castration.

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target

BACKGROUND: The androgen receptor (AR) is a major drug target in prostate cancer (PCa). We profiled the AR-regulated kinome to identify clinically relevant and druggable effectors of AR signaling.

METHODS: Using genome-wide approaches, we interrogated all AR regulated kinases. Among these, choline kinase alpha (CHKA) expression was evaluated in benign (n = 195), prostatic intraepithelial neoplasia (PIN) (n = 153) and prostate cancer (PCa) lesions (n = 359). We interrogated how CHKA regulates AR signaling using biochemical assays and investigated androgen regulation of CHKA expression in men with PCa, both untreated (n = 20) and treated with an androgen biosynthesis inhibitor degarelix (n = 27). We studied the effect of CHKA inhibition on the PCa transcriptome using RNA sequencing and tested the effect of CHKA inhibition on cell growth, clonogenic survival and invasion. Tumor xenografts (n = 6 per group) were generated in mice using genetically engineered prostate cancer cells with inducible CHKA knockdown. Data were analyzed with χ(2) tests, Cox regression analysis, and Kaplan-Meier methods. All statistical tests were two-sided.

RESULTS: CHKA expression was shown to be androgen regulated in cell lines, xenografts, and human tissue (log fold change from 6.75 to 6.59, P = .002) and was positively associated with tumor stage. CHKA binds directly to the ligand-binding domain (LBD) of AR, enhancing its stability. As such, CHKA is the first kinase identified as an AR chaperone. Inhibition of CHKA repressed the AR transcriptional program including pathways enriched for regulation of protein folding, decreased AR protein levels, and inhibited the growth of PCa cell lines, human PCa explants, and tumor xenografts.

CONCLUSIONS: CHKA can act as an AR chaperone, providing, to our knowledge, the first evidence for kinases as molecular chaperones, making CHKA both a marker of tumor progression and a potential therapeutic target for PCa.

Behavioural reactivity of ewes and lambs during partial and total social isolation

This work investigated the differences in the reactivity of Sarda (primiparous n= 18, multiparous n= 17) and Dorset (multiparous n= 8) breeds of sheep and their singleton lambs to two challenging test situations involving a mother-lamb partial separation test and an isolation test. Non-parametric analysis used single behavioural variables and fear scores to evaluate the effect of parity, sex of lambs, and the association between mother-lamb behaviour. Amongst ewes, Dorset were characterised by a more calm temperament while Sarda (especially primiparous ewes) were more active in their response to challenge (i.e. more attempts to escape). As with their dams, lambs reflected to a certain extent this divergence and overall during isolation lamb fear score was on average significantly higher than dams. Correlations between measures of behavioural reactivity across tests were carried out to search for predictive measures of fear. A very strong correlation emerged linking vocalisation to locomotor activity. Vocalisation could be a good candidate as predictor factor of an active reaction of sheep to a fearful situation.

Gene regulatory mechanisms underpinning prostate cancer susceptibility

Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.