An investigation into the role of sex chromosome synapsis in meiotic sex chromosome inactivation and fertility

During male meiosis in a number of species, the sex chromosomes become transcriptionally inactive (termed meiotic sex chromosome inactivation, or MSCI) and form a peripheral, densely staining structure termed the sex body. The function of MSCI is not known, but it may serve to silence 'poisonous' sex-linked genes, or to prevent the asynapsed portions of the sex chromosomes from triggering a checkpoint that monitors synapsis, recombination, or both. It has been postulated that MSCI is mediated by the Xist gene, and that Y chromosome inactivation proceeds by 'quasi-cis' spreading of Xist RNA from the X chromosome to the Y chromosome via the synapsed pseudoautosomal regions. The purpose of the present study was to examine the quasi-cis hypothesis, by analysing MSCI in Xist-disrupted spermatocytes, and Y chromosome inactivation in spermatocytes with high levels of X-Y synaptic failure. The first two chapters were aimed at identifying an MSCI marker that could be used to carry out the experiments described above. The MSCI-specificity of three sex body proteins: ASY, XMR/XLR and XY77 was examined by analysing the expression of each in oocytes from XYTdym1 females. The sex chromosomes in these oocytes failed to exhibit MSCI and were therefore suitable as negative controls. ASY and XMR/XLR coated the asynapsed X chromosome in XYTdym1 oocytes and also the asynapsed autosomes in T(2;5)72H oocytes, indicating that their presence in the sex body is related to the asynaptic and not transcriptionally inactive state of the sex chromosomes. XY77, in contrast, was sex body-specific. Next, the quasi-cis model was investigated by examination of MSCI in Xist-disrupted males and in males with sex chromosome synaptic failure (XYYd1, XYY*x). MSCI and sex body formation proceeded normally in the absence of Xist, but both were disrupted in XYYd1 spermatocytes. XYYd1 spermatocytes exhibiting defects in sex body formation and/or MSCI were eliminated between mid and late pachytene, indicating that MSCI is indispensable for meiosis and that it is disrupted by excess sex chromatin. Finally, an inherited genetic effect was characterised that could partially circumvent the pachytene checkpoint in XY*O mice. This effect allowed the normally sterile XY*O males to be fertile. The fertility was found to be due to the inheritance of an autosomal, dominant C3H factor (the major factor) together with a recessive MFl factor. Inheritance of a second, dominantly-acting C3H allele (the minor factor) further augmented the sperm counts of the XY*O males. Neither of the C3H factors was Hstl, a gene that confers fertility to interspecific hybrid male mice. Inheritance of these XY*O fertility factors was unable to restore fertility in XY*YTdym1 males, possibly due to the additional defects in MSCI that these males would be expected to experience

Clinical trial metadata:Defining and extracting metadata on the design, conduct, results and costs of 125 randomised clinical trials funded by the National Institute for Health Research Health Technology Assessment programme

Background:  By 2011, the Health Technology Assessment (HTA) programme had published the results of over 100 trials with another 220 in progress. The aim of the project was to develop and pilot ‘metadata’ on clinical trials funded by the HTA programme.   Objectives: The aim of the project was to develop and pilot questions describing clinical trials funded by the HTA programme in terms of it meeting the needs of the NHS with scientifically robust studies. The objectives were to develop relevant classification systems and definitions for use in answering relevant questions and to assess their utility.   Data sources: Published monographs and internal HTA documents.   Review methods: A database was developed, ‘populated’ using retrospective data and used to answer questions under six prespecified themes. Questions were screened for feasibility in terms of data availability and/or ease of extraction. Answers were assessed by the authors in terms of completeness, success of the classification system used and resources required. Each question was scored to be retained, amended or dropped.    Results: One hundred and twenty-five randomised trials were included in the database from 109 monographs. Neither the International Standard Randomised Controlled Trial Number nor the term ‘randomised trial’ in the title proved a reliable way of identifying randomised trials. Only limited data were available on how the trials aimed to meet the needs of the NHS. Most trials were shown to follow their protocols but updates were often necessary as hardly any trials recruited as planned. Details were often lacking on planned statistical analyses, but we did not have access to the relevant statistical plans. Almost all the trials reported on cost-effectiveness, often in terms of both the primary outcome and quality-adjusted life-years. The cost of trials was shown to depend on the number of centres and the duration of the trial. Of the 78 questions explored, 61 were well answered, 33 fully with 28 requiring amendment were the analysis updated. The other 17 could not be answered with readily available data.   Limitations: The study was limited by being confined to 125 randomised trials by one funder.   Conclusions: Metadata on randomised controlled trials can be expanded to include aspects of design, performance, results and costs. The HTA programme should continue and extend the work reported here

Quadratic estimates and functional calculi for inhomogeneous first-order operators and applications to boundary value problems for Schrödinger equations

We develop a holomorphic functional calculus for first-order operators DB to solve boundary value problems for Schrödinger equations −div A∇u + aVu = 0 in the upper half-space $ℝ^{n+1}_+$ when n ≥ 3. This relies on quadratic estimates for DB, which are proved for coefficients A, a, V that are independent of the transversal direction to the boundary, and comprised of a complex-elliptic pair A, a that are bounded and measurable, and a singular potential V in the reverse Hölder class $B^{\frac{n}{2}} (ℝ^n)$. The square function bounds are also shown to be equivalent to non-tangential maximal function bounds. This allows us to prove that the Dirichlet regularity and Neumann boundary value problems with $L^2( ℝ^n)$-data are well-posed if and only if certain boundary trace operators defined by the functional calculus are isomorphisms. We prove this property when the coefficient matrices A and a are either a Hermitian or block structure. More generally, the set of all complex-elliptic A for which the boundary value problems are well-posed is shown to be open in $L^∞$. We also prove these solutions coincide with those generated from the Lax–Milgram Theorem. Furthermore, we extend this theory to prove quadratic estimates for the magnetic Schrödinger operator (∇ + ib)∗A(∇ + ib) when the magnetic field curl (b) is in the reverse Hölder class $B^{\frac{n}{2}} (ℝ^n)$

Evidence-based medicine, "placebos" and the homeopathy controversy

Homeopathic treatment has been available on the UK’s National Health Service (NHS) since 1948. In recent years the continued provision of homeopathy through the NHS has been increasingly questioned as part of the ascendency of evidence-based medicine (EBM). Indeed, in 2009 the House of Common’s Science and Technology committee commenced an ‘Evidence Check’ inquiry into Government policy supporting the NHS provision of homeopathic treatments. The controversy over whether homeopathic treatments ‘really’ work and whether they should be available through the NHS has generated much debate: at the heart of the controversy are questions about the nature of evidence in medicine, the validity of randomised trials and the nature and utility of ‘placebo effects’. Critics of homeopathy put forward the simple argument that best available evidence shows homeopathic treatments to be equivalent to placebo, and therefore conclude that it should not be available through publically funded healthcare. This thesis presents a critical examination of the concepts of EBM and ‘placebos’ and re-evaluates their role in the controversy around homeopathy. This thesis examines what kind of foundation the EBM philosophy of evidence provides for the arguments made in the controversy, and the role that ‘placebos’ play as both an evidential and normative standard. There are two basic arguments: first, that the arguments justifying the EBM philosophy of evidence are fundamentally unclear, but also that the interpretation given to EBM, in debates about homeopathy, cannot be sustained. Second, that the concept of ‘placebos’ should be abandoned entirely: a framework is developed for talking about the effectiveness of treatments that removes much confusion about the epistemological and ethical standards that effective treatments should be held to. In addition to attempting to provide conceptual clarity to the controversy, the main conclusion is that the Science and Technology Committee have (on the basis of their own assumptions) understated their evidential arguments, by ignoring mechanistic evidence for whether homeopathic treatments are effective, and they have overstated their ethical arguments, they do not provide good reasons to remove provision of homeopathic treatment through the NHS

Control freaks-signals and cues governing the regulation of virulence in attaching and effacing pathogens

Enterohaemorrhagic Escherichia coli (EHEC) mediates disease using a type 3 secretion system (T3SS), which is encoded on the locus of enterocyte effacement (LEE) and is tightly controlled by master regulators. This system is further modulated by a number of signals that help to fine-tune virulence, including metabolic, environmental and chemical signals. Since the LEE, and its master regulator, Ler, were established there have been numerous scientific advancements in understanding the regulation and expression of virulence factors in EHEC. This review will discuss the recent advancements in this field since our previous review, with a focus on transcriptional regulation of the LEE

Evidence-based medicine, "placebos" and the homeopathy controversy

Homeopathic treatment has been available on the UK’s National Health Service (NHS) since 1948. In recent years the continued provision of homeopathy through the NHS has been increasingly questioned as part of the ascendency of evidence-based medicine (EBM). Indeed, in 2009 the House of Common’s Science and Technology committee commenced an ‘Evidence Check’ inquiry into Government policy supporting the NHS provision of homeopathic treatments. The controversy over whether homeopathic treatments ‘really’ work and whether they should be available through the NHS has generated much debate: at the heart of the controversy are questions about the nature of evidence in medicine, the validity of randomised trials and the nature and utility of ‘placebo effects’. Critics of homeopathy put forward the simple argument that best available evidence shows homeopathic treatments to be equivalent to placebo, and therefore conclude that it should not be available through publically funded healthcare. This thesis presents a critical examination of the concepts of EBM and ‘placebos’ and re-evaluates their role in the controversy around homeopathy. This thesis examines what kind of foundation the EBM philosophy of evidence provides for the arguments made in the controversy, and the role that ‘placebos’ play as both an evidential and normative standard. There are two basic arguments: first, that the arguments justifying the EBM philosophy of evidence are fundamentally unclear, but also that the interpretation given to EBM, in debates about homeopathy, cannot be sustained. Second, that the concept of ‘placebos’ should be abandoned entirely: a framework is developed for talking about the effectiveness of treatments that removes much confusion about the epistemological and ethical standards that effective treatments should be held to. In addition to attempting to provide conceptual clarity to the controversy, the main conclusion is that the Science and Technology Committee have (on the basis of their own assumptions) understated their evidential arguments, by ignoring mechanistic evidence for whether homeopathic treatments are effective, and they have overstated their ethical arguments, they do not provide good reasons to remove provision of homeopathic treatment through the NHS

Plastic circuits: regulatory flexibility in fine tuning pathogen success

Bacterial pathogens employ diverse fitness and virulence mechanisms to gain an advantage in competitive niches. These lifestyle-specific traits require integration into the regulatory network of the cell and are often controlled by pre-existing transcription factors. In this review, we highlight recent advances that have been made in characterizing this regulatory flexibility in prominent members of the Enterobacteriaceae. We focus on the direct global interactions between transcription factors and their target genes in pathogenic Escherichia coli and Salmonella revealed using chromatin immunoprecipitation coupled with next-generation sequencing. Furthermore, the implications and advantages of such regulatory adaptations in benefiting distinct pathogenic lifestyles are discussed

Black carbon physical and optical properties across northern India during pre-monsoon and monsoon seasons

Black carbon (BC) is known to have major impacts on both climate and human health and is therefore of global importance, particularly in regions close to large populations that have strong sources. The size-resolved mixing state of BC-containing particles was characterised using a single-particle soot photometer (SP2). The study focusses on the Indo-Gangetic Plain (IGP) during the pre-monsoon and monsoon seasons. Data presented are from the UK Facility for Airborne Atmospheric Measurements BAe-146 research aircraft that performed flights during the pre-monsoon (11 and 12 June) and monsoon (30 June to 11 July) seasons of 2016. Over the IGP, BC mass concentrations were greater (1.95 µg m−3) compared to north-west India (1.50 µg m−3) and north-east India (0.70 µg m−3) during the pre-monsoon season. Across northern India, two distinct BC modes were recorded; a mode of small BC particles (core diameter <0.16 µm and coating thickness <50 nm) and a mode of moderately coated BC (core diameter <0.22 µm and coating thickness of 50–200 nm). The IGP and north-east India locations exhibited moderately coated black carbon particles with enhanced coating thicknesses, core sizes, mass absorption cross sections, and scattering enhancement values compared to much lower values present in the north-west. The coating thickness and mass absorption cross section increased with altitude (13 %) compared to those in the boundary layer. As the monsoon arrived across the region, mass concentration of BC decreased over the central IGP and north-east locations (38 % and 28 % respectively), whereas for the north-west location BC properties remained relatively consistent. Post-monsoon onset, the coating thickness, core size, mass absorption cross section, and scattering enhancement values were all greatest over the central IGP much like the pre-monsoon season but were considerably reduced over both north-east and north-west India. Increases in mass absorption cross section through the atmospheric column were still present during the monsoon for the north-west and central IGP locations, but less so over the north-east due to lack of long-range transport aerosol aloft. Across the Indo-Gangetic Plain and north-east India during the pre-monsoon and monsoon seasons, solid-fuel (wood burning) emissions form the greatest proportion of BC with moderately coated particles. However, as the monsoon develops in the north-east there was a switch to small uncoated BC particles indicative of traffic emissions, but the solid-fuel emissions remained in the IGP into the monsoon. For both seasons in the north-west, traffic emissions form the greatest proportion of BC particles. Our findings will prove important for greater understanding of the BC physical and optical properties, with important consequences for the atmospheric radiative forcing of BC-containing particles. The findings will also help constrain the regional aerosol models for a variety of applications such as space-based remote sensing, chemistry transport modelling, air quality, and BC source and emission inventories

Validity and Reliability of Firefighting Simulation Test Performance

To assess the validity and reliability of a firefighting simulation test (FFST). Sixty-nine operational firefighters completed a best-effort FFST on one occasion and twenty-two participants completed a further FFST. All participants completed a maximal treadmill test to determine cardiorespiratory fitness (VO2max). Time to complete the FFST demonstrated a strong inverse relationship with VO2max (r = -0.73), although the prediction error was high. Reliability of the FFST was high (r = 0.84, p = 0.01), demonstrating a coefficient of variation of 4.5%. The FFST demonstrated reasonable validity as a surrogate assessment of cardiorespiratory fitness for firefighting. The FFST also demonstrated good reliability. Given the apparent magnitude of the prediction error, the FFST would be best used as a training tool, rather than as a primary means of assessing cardiorespiratory fitness for firefighting