Intrachromosomal excision of a hybrid Ds element induces large genomic deletions in Arabidopsis

Transposon activity is known to cause chromosome rearrangements in the host genome. Surprisingly, extremely little is known about Dissociation (Ds)-induced chromosome rearrangements in Arabidopsis, where Ds is intensively used for insertional mutagenesis. Here, we describe three Arabidopsis mutants with reduced fertility and propose that excision of a hybrid Ds element induced a large genomic deletion flanking Ds. In the mutants anat and haumea, the deletion mechanism consists of a local Ds transposition from replicated into unreplicated DNA followed by Ds excision, where one end of the newly transposed element and one end of the Ds transposon at the donor site served as substrate for transposase. Excision of this hybrid element reminiscent of a macrotransposon leads to loss of the chromosomal piece located between the two ends, including one full Ds element and the flanking genomic sequence. This mechanism was found to be responsible for several other deletions and occurs at a genetically trackable frequency. Thus, it could be applied to efficiently generate deletions of various sizes in the vicinity of any existing Ds element present in the genome. In the mutant tons missing, a mechanism that involves endogenous repetitive sequences caused a large flanking deletion at a position unlinked to the starter locus. Our study of Ds transposition in Arabidopsis revealed previously undescribed mechanisms that lead to large genomic deletions flanking Ds elements, which may contribute to genome dynamics and evolution

Magnetic Fields of Spherical Compact Stars in Braneworld

We study the dipolar magnetic field configuration in dependence on brane tension and present solutions of Maxwell equations in the internal and external background spacetime of a magnetized spherical star in a Randall-Sundrum II type braneworld. The star is modelled as sphere consisting of perfect highly magnetized fluid with infinite conductivity and frozen-in dipolar magnetic field. With respect to solutions for magnetic fields found in the Schwarzschild spacetime brane tension introduces enhancing corrections both to the interior and the exterior magnetic field. These corrections could be relevant for the magnetic fields of magnetized compact objects as pulsars and magnetars and may provide the observational evidence for the brane tension through the modification of formula for magneto-dipolar emission which gives amplification of electromagnetic energy loss up to few orders depending on the value of the brane tension.Comment: 11 pages, 5 figures, 1 tabl

Virtual patients design and its effect on clinical reasoning and student experience : a protocol for a randomised factorial multi-centre study

Background Virtual Patients (VPs) are web-based representations of realistic clinical cases. They are proposed as being an optimal method for teaching clinical reasoning skills. International standards exist which define precisely what constitutes a VP. There are multiple design possibilities for VPs, however there is little formal evidence to support individual design features. The purpose of this trial is to explore the effect of two different potentially important design features on clinical reasoning skills and the student experience. These are the branching case pathways (present or absent) and structured clinical reasoning feedback (present or absent). Methods/Design This is a multi-centre randomised 2x2 factorial design study evaluating two independent variables of VP design, branching (present or absent), and structured clinical reasoning feedback (present or absent).The study will be carried out in medical student volunteers in one year group from three university medical schools in the United Kingdom, Warwick, Keele and Birmingham. There are four core musculoskeletal topics. Each case can be designed in four different ways, equating to 16 VPs required for the research. Students will be randomised to four groups, completing the four VP topics in the same order, but with each group exposed to a different VP design sequentially. All students will be exposed to the four designs. Primary outcomes are performance for each case design in a standardized fifteen item clinical reasoning assessment, integrated into each VP, which is identical for each topic. Additionally a 15-item self-reported evaluation is completed for each VP, based on a widely used EViP tool. Student patterns of use of the VPs will be recorded. In one centre, formative clinical and examination performance will be recorded, along with a self reported pre and post-intervention reasoning score, the DTI. Our power calculations indicate a sample size of 112 is required for both primary outcomes

Period-doubling bifurcation in strongly anisotropic Bianchi I quantum cosmology

We solve the Wheeler-DeWitt equation for the minisuperspace of a cosmological model of Bianchi type I with a minimally coupled massive scalar field $\phi$ as source by generalizing the calculation of Lukash and Schmidt [1]. Contrarily to other approaches we allow strong anisotropy. Combining analytical and numerical methods, we apply an adiabatic approximation for $\phi$, and as new feature we find a period-doubling bifurcation. This bifurcation takes place near the cosmological quantum boundary, i.e., the boundary of the quasiclassical region with oscillating $\psi$-function where the WKB-approximation is good. The numerical calculations suggest that such a notion of a ``cosmological quantum boundary'' is well-defined, because sharply beyond that boundary, the WKB-approximation is no more applicable at all. This result confirms the adequateness of the introduction of a cosmological quantum boundary in quantum cosmology.Comment: Latest update of the paper at http://www.physik.fu-berlin.de/~mbach/publics.html#

Fusion of green fluorescent protein to the C-terminus of granulysin alters its intracellular localization in comparison to the native molecule

The engineering of green fluorescent protein (GFP) fusion constructs in order to visibly tag a protein of interest has become a commonly used cell biology technique. Although caveats to this approach are obvious, literature reports in which the chimeric molecule behaves differently than the native molecule are scant. This brief report describes one such case. Granulysin, a small lytic and antimicrobial protein produced by cytotoxic lymphocytes, traffics to the regulated secretory system and is subsequently released from cells upon proper stimulus. In an attempt to elucidate mechanisms by which it accumulates in and is released from cytolytic granules, GFP was fused to the C-terminus of granulysin and expressed in an NK cell line. A control construct expressing the native protein was similarly expressed. The data demonstrate that, while the fusion protein is expressed and secreted, its subcellular localization is altered in comparison to native granulysin. Thus, the addition of GFP to the C-terminus of granulysin obscures the signal(s) that cytotoxic lymphocytes use to sort it to the regulated secretory pathway despite its normal biosynthesis and secretion. This example is offered as a cautionary account for other researchers who contemplate using this technology

Phosphorylation of the androgen receptor is associated with reduced survival in hormonerefractory prostate cancer patients

Cell line studies demonstrate that the PI3K/Akt pathway is upregulated in hormone-refractory prostate cancer (HRPC) and can result in phosphorylation of the androgen receptor (AR). The current study therefore aims to establish if this has relevance to the development of clinical HRPC. Immunohistochemistry was employed to investigate the expression and phosphorylation status of Akt and AR in matched hormone-sensitive and -refractory prostate cancer tumours from 68 patients. In the hormone-refractory tissue, only phosphorylated AR (pAR) was associated with shorter time to death from relapse (<i>P</i>=0.003). However, when an increase in expression in the transition from hormone-sensitive to -refractory prostate cancer was investigated, an increase in expression of PI3K was associated with decreased time to biochemical relapse (<i>P</i>=0.014), and an increase in expression of pAkt<sup>473</sup> and pAR<sup>210</sup> were associated with decreased disease-specific survival (<i>P</i>=0.0019 and 0.0015, respectively). Protein expression of pAkt<sup>473</sup> and pAR<sup>210</sup> also strongly correlated (<i>P</i><0.001, c.c.=0.711) in the hormone-refractory prostate tumours. These results provide evidence using clinical specimens, that upregulation of the PI3K/Akt pathway is associated with phosphorylation of the AR during development of HRPC, suggesting that this pathway could be a potential therapeutic target

Brain glutamate and gamma-aminobutyrate (GABA) metabolism in thiamin-deficient rats

The brain metabolism of glutamate and gamma-aminobutyrate (GABA) was investigated in thiamin-deficient and pair-fed control rats, in order to determine whether the GABA shunt may provide an important alternative to 2-oxo-glutarate dehydrogenase (EC 1.2.4.2) in energy-yielding metabolism in thiamin deficiency. Brains from thiamin-deficient animals contained less glutamate, 2-oxo-glutarate and GABA than those from control animals. The brain content of ATP was unaffected by thiamin deficiency. After intracerebroventricular injection of [14C]glutamate, the specific radioactivity of GABA in the brains from deficient animals was 45-50% higher than that in controls, suggesting a considerable increase in the metabolic flux through the GABA shunt in thiamin deficiency. Brain GABA showed a marked circumannual variation, with a peak in mid-summer and a minimum value in mid-winter

Hahn's Symmetric Quantum Variational Calculus

We introduce and develop the Hahn symmetric quantum calculus with applications to the calculus of variations. Namely, we obtain a necessary optimality condition of Euler-Lagrange type and a sufficient optimality condition for variational problems within the context of Hahn's symmetric calculus. Moreover, we show the effectiveness of Leitmann's direct method when applied to Hahn's symmetric variational calculus. Illustrative examples are provided.Comment: This is a preprint of a paper whose final and definite form will appear in the international journal Numerical Algebra, Control and Optimization (NACO). Paper accepted for publication 06-Sept-201

Epidemiology and reporting characteristics of preclinical systematic reviews

In an effort to better utilize published evidence obtained from animal experiments, systematic reviews of preclinical studies are increasingly more common-along with the methods and tools to appraise them (e.g., SYstematic Review Center for Laboratory animal Experimentation [SYRCLE's] risk of bias tool). We performed a cross-sectional study of a sample of recent preclinical systematic reviews (2015-2018) and examined a range of epidemiological characteristics and used a 46-item checklist to assess reporting details. We identified 442 reviews published across 43 countries in 23 different disease domains that used 26 animal species. Reporting of key details to ensure transparency and reproducibility was inconsistent across reviews and within article sections. Items were most completely reported in the title, introduction, and results sections of the reviews, while least reported in the methods and discussion sections. Less than half of reviews reported that a risk of bias assessment for internal and external validity was undertaken, and none reported methods for evaluating construct validity. Our results demonstrate that a considerable number of preclinical systematic reviews investigating diverse topics have been conducted; however, their quality of reporting is inconsistent. Our study provides the justification and evidence to inform the development of guidelines for conducting and reporting preclinical systematic reviews