Directional Next-Generation RNA Sequencing and Examination of Premature Termination Codon Mutations in Endoglin/Hereditary Haemorrhagic Telangiectasia

Hereditary haemorrhagic telangiectasia (HHT) is a disease characterised by abnormal vascular structures, and most commonly caused by mutations in ENG, ACVRL1 or SMAD4 encoding endothelial cell-expressed proteins involved in TGF-β superfamily signalling. The majority of mutations reported on the HHT mutation database are predicted to lead to stop codons, either due to frameshifts or direct nonsense substitutions. The proportion is higher for ENG (67%) and SMAD4 (65%) than for ACVRL1 (42%), p < 0.0001. Here, by focussing on ENG, we report why conventional views of these mutations may need to be revised. Of the 111 stop codon-generating ENG mutations, on ExPASy translation, all except one were premature termination codons (PTCs), sited at least 50-55 bp upstream of the final exon-exon boundary of the main endoglin isoform, L-endoglin. This strongly suggests that the mutated RNA species will undergo nonsense-mediated decay. We provide new in vitro expression data to support dominant negative activity of stable truncated endoglin proteins but suggest these will not generate HHT: the single natural stop codon mutation in L-endoglin (sited within 50-55 nucleotides of the final exon-exon boundary) is unlikely to generate functional protein since it replaces the entire transmembrane domain, as would 8 further natural stop codon mutations, if the minor S-endoglin isoform were implicated in HHT pathogenesis. Finally, next-generation RNA sequencing data of 7 different RNA libraries from primary human endothelial cells demonstrate that multiple intronic regions of ENG are transcribed. The potential consequences of heterozygous deletions or duplications of such regions are discussed. These data support the haploinsufficiency model for HHT pathogenesis, explain why final exon mutations have not been detected to date in HHT, emphasise the potential need for functional examination of non-PTC-generating mutations, and lead to proposals for an alternate stratification system of mutational types for HHT genotype-phenotype correlations

Health effects of home energy efficiency interventions in England: a modelling study

Objective: To assess potential public health impacts of changes to indoor air quality and temperature due to energy efficiency retrofits in English dwellings to meet 2030 carbon reduction targets. Design: Health impact modelling study. Setting: England. Participants: English household population. Intervention: Three retrofit scenarios were modelled: (1) fabric and ventilation retrofits installed assuming building regulations are met. (2) As with scenario (1) but with additional ventilation for homes at risk of poor ventilation. (3) As with scenario (1) but with no additional ventilation to illustrate the potential risk of weak regulations and non-compliance. Main Outcome: Primary outcomes were changes in quality adjusted life years (QALYs) over 50 years from cardiorespiratory diseases, lung cancer, asthma and common mental disorders due to changes in indoor air pollutants, including: second-hand tobacco smoke, PM2.5 from indoor and outdoor sources, radon, mould, and indoor winter temperatures. Results: The modelling study estimates showed that scenario (1) resulted in positive effects on net mortality and morbidity of 2,241 (95% credible intervals (CI) 2,085 to 2,397) QALYs per 10,000 persons over 50 years due to improved temperatures and reduced exposure to indoor pollutants, despite an increase in exposure to outdoor–generated PM2.5. Scenario (2) resulted in a negative impact of -728 (95% CI -864 to -592) QALYs per 10,000 persons over 50 years due to an overall increase in indoor pollutant exposures. Scenario (3) resulted in -539 (95% CI -678 to -399) QALYs per 10,000 persons over 50 years due to an increase in indoor exposures despite targeting. Conclusions: If properly implemented alongside ventilation, energy efficiency retrofits in housing can improve health by reducing exposure to cold and air pollutants. Maximising the health benefits requires careful understanding of the balance of changes in pollutant exposures, highlighting the importance of ventilation to mitigate the risk of poor indoor air quality

Geophysical characterization of derelict coalmine workings and mineshaft detection: a case study from Shrewsbury, United Kingdom

A study site of derelict coalmine workings near Shrewsbury, United Kingdom was the focus for multi‐phase, near‐surface geophysical investigations. Investigation objectives were: 1) site characterization for remaining relict infrastructure foundations, 2) locate an abandoned coalmine shaft, 3) determine if the shaft was open, filled or partially filled and 4) determine if the shaft was capped (and if possible characterize the capping material). Phase one included a desktop study and 3D microgravity modelling of the relict coalmine shaft thought to be on site. In phase two, electrical and electromagnetic surveys to determine site resistivity and conductivity were acquired together with fluxgate gradiometry and an initial microgravity survey. Phase three targeted the phase two geophysical anomalies and acquired high‐resolution self potential and ground penetrating radar datasets. The phased‐survey approach minimised site activity and survey costs. Geophysical results were compared and interpreted to characterize the site, the microgravity models were used to validate interpretations. Relict buildings, railway track remains with associated gravel and a partially filled coalmine shaft were located. Microgravity proved optimal to locate the mineshaft with radar profiles showing ‘side‐swipe’ effects from the mineshaft that did not directly underlie survey lines. Geophysical interpretations were then verified with subsequent geotechnical intrusive investigations. Comparisons of historical map records with intrusive geotechnical site investigations show care must be taken using map data alone, as the latter mineshaft locations was found to be inaccurate

Mitochondrial network state scales mtDNA genetic dynamics

Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The role of the resulting mitochondrial networks in the time evolution of the cellular proportion of mutated mtDNA molecules (heteroplasmy), and cell-to-cell variability in heteroplasmy (heteroplasmy variance), remains incompletely understood. Heteroplasmy variance is particularly important since it modulates the number of pathological cells in a tissue. Here, we provide the first wide-reaching theoretical framework which bridges mitochondrial network and genetic states. We show that, under a range of conditions, the (genetic) rate of increase in heteroplasmy variance and de novo mutation are proportionally modulated by the (physical) fraction of unfused mitochondria, independently of the absolute fission-fusion rate. In the context of selective fusion, we show that intermediate fusion/fission ratios are optimal for the clearance of mtDNA mutants. Our findings imply that modulating network state, mitophagy rate and copy number to slow down heteroplasmy dynamics when mean heteroplasmy is low could have therapeutic advantages for mitochondrial disease and healthy aging

Predicting concrete durability from its absorption

This paper discusses the current approach for specifying the durability of concrete in structures. The shortcomings of the use of bulk parameters such as strength, water/binder ratio and binder content to specify durability are discussed. Studies carried out over the last 10 years at Dundee University, using simple permeation tests, which are sensitive to curing, cement type and grade of concrete, have shown close association between permeation properties and the durability of concrete. This paper deals with the measurement of concrete durability by the Dundeemodified Initial Surface Absorption Test (ISAT). A wide range of concrete mixes made with ordinary portland cement and blends with pulverized-fuel ash (PFA) and ground-granulated blastfurnace slag were designed. The duration of moist curing was varied from 0 to 28 days, and the maximum aggregate size from 5 to 40mm. All mixes were tested for absorptivity and aspects of durability including freeze/thaw resistance, carbonation, chloride ingress and mechanical wear. The results show that the absorptivity of concrete, measured with the ISAT, could be used as an accurate specification for concrete durability, irrespective of curing, grade or mix constituents. A tentative surface absorptivity classification for durability has been proposed

Evolution of cell-to-cell variability in stochastic, controlled, heteroplasmic mtDNA populations

Populations of physiologically vital mitochondrial DNA (mtDNA) molecules evolve in cells under control from the nucleus. The evolution of populations of mixed mtDNA types is complicated and poorly understood, and variability of these controlled admixtures plays a central role in the inheritance and onset of genetic disease. Here, we develop a mathematical theory describing the evolution of, and variability in, these stochastic populations for any type of cellular control, showing that cell-to-cell variability in mtDNA and mutant load inevitably increases with time, according to rates that we derive and which are notably independent of the mechanistic details of feedback signaling. We show with a set of experimental case studies that this theory explains disparate quantitative results from classical and modern experimental and computational research on heteroplasmy variance in different species. We demonstrate that our general model provides a host of specific insights, including a modification of the often-used but hard-to-interpret Wright formula to correspond directly to biological observables, the ability to quantify selective and mutational pressure in mtDNA populations, and characterization of the pronounced variability inevitably arising from the action of possible mtDNA quality-control mechanisms. Our general theoretical framework, supported by existing experimental results, thus helps us to understand and predict the evolution of stochastic mtDNA populations in cell biology

Quantitative characterization of plastic deformation of single diamond crystals: A high pressure high temperature (HPHT) experimental deformation study combined with electron backscatter diffraction (EBSD)

We report the results of a high-pressure high-temperature (HPHT) experimental investigation into the deformation of diamonds using the D-DIA apparatus. Electron backscatter diffraction (EBSD) data confirm that well-defined 300–700 nm wide {111} slip lamellae are in fact deformation micro-twins with a 60° rotation around a axis. Such twins formed at high confining pressures even without any apparatus-induced differential stress; mechanical anisotropy within the cell assembly was sufficient for their formation with very little subsequent lattice bending ( slip system dominates as expected for the face-centred cubic (FCC) structure of diamond. Slip occurs on multiple {111} planes resulting in rotation around axes. Deformation microstructure characteristics depend on the orientation of the principal stress axes and finite strain but are independent of confining pressure and nitrogen content. All of the uniaxially deformed samples took on a brown colour, irrespective of their initial nitrogen characteristics. This is in contrast to the two quasi-hydrostatic experiments, which retained their original colour (colourless for nitrogen free diamond, yellow for single substitutional nitrogen, Type Ib diamond) despite the formation of {111} twin lamellae. Comparison of our experimental data with those from two natural brown diamonds from Finsch mine (South Africa) shows the same activation of the dominant slip system. However, no deformation twin lamellae are present in the natural samples. This difference may be due to the lower strain rates experienced by the natural samples investigated. Our study shows the applicability and potential of this type of analysis to the investigation of plastic deformation of diamonds under mantle conditions

Development of models of care coordination for rare conditions: a qualitative study.

INTRODUCTION: Improving care coordination for people with rare conditions may help to reduce burden on patients and carers and improve the care that patients receive. We recently developed a taxonomy of different ways of coordinating care for rare conditions. It is not yet known which models of care coordination are appropriate in different situations. This study aimed to: (1) explore what types of care coordination may be appropriate in different situations, and (2) use these findings to develop hypothetical models of care coordination for rare conditions. METHODS: To explore appropriateness of different types of care coordination, we conducted interviews (n = 30), four focus groups (n = 22) and two workshops (n = 27) with patients, carers, healthcare professionals, commissioners, and charity representatives. Participants were asked about preferences, benefits and challenges, and the factors influencing coordination. Thematic analysis was used to develop hypothetical models of care coordination. Models were refined following feedback from workshop participants. RESULTS: Stakeholders prefer models of care that: are nationally centralised or a hybrid of national and local care, involve professionals collaborating to deliver care, have clear roles and responsibilities outlined (including administrative, coordinator, clinical and charity roles), provide access to records and offer flexible appointments (in terms of timing and mode). Many factors influenced coordination, including those relating to the patient (e.g., condition complexity, patient's location and ability to coordinate their own care), the healthcare professional (e.g., knowledge and time), the healthcare environment (e.g., resources) and societal factors (e.g., availability of funding). We developed and refined ten illustrative hypothetical models of care coordination for rare conditions. CONCLUSION: Findings underline that different models of care coordination may be appropriate in different situations. It is possible to develop models of care coordination which are tailored to the individual in context. Findings may be used to facilitate planning around which models of care coordination may be appropriate in different services or circumstances. Findings may also be used by key stakeholders (e.g. patient organisations, clinicians and service planners) as a decision-making tool

Development of models of care coordination for rare conditions: a qualitative study.

INTRODUCTION: Improving care coordination for people with rare conditions may help to reduce burden on patients and carers and improve the care that patients receive. We recently developed a taxonomy of different ways of coordinating care for rare conditions. It is not yet known which models of care coordination are appropriate in different situations. This study aimed to: (1) explore what types of care coordination may be appropriate in different situations, and (2) use these findings to develop hypothetical models of care coordination for rare conditions. METHODS: To explore appropriateness of different types of care coordination, we conducted interviews (n = 30), four focus groups (n = 22) and two workshops (n = 27) with patients, carers, healthcare professionals, commissioners, and charity representatives. Participants were asked about preferences, benefits and challenges, and the factors influencing coordination. Thematic analysis was used to develop hypothetical models of care coordination. Models were refined following feedback from workshop participants. RESULTS: Stakeholders prefer models of care that: are nationally centralised or a hybrid of national and local care, involve professionals collaborating to deliver care, have clear roles and responsibilities outlined (including administrative, coordinator, clinical and charity roles), provide access to records and offer flexible appointments (in terms of timing and mode). Many factors influenced coordination, including those relating to the patient (e.g., condition complexity, patient's location and ability to coordinate their own care), the healthcare professional (e.g., knowledge and time), the healthcare environment (e.g., resources) and societal factors (e.g., availability of funding). We developed and refined ten illustrative hypothetical models of care coordination for rare conditions. CONCLUSION: Findings underline that different models of care coordination may be appropriate in different situations. It is possible to develop models of care coordination which are tailored to the individual in context. Findings may be used to facilitate planning around which models of care coordination may be appropriate in different services or circumstances. Findings may also be used by key stakeholders (e.g. patient organisations, clinicians and service planners) as a decision-making tool

Effects of intermediate scales on renormalization group running of fermion observables in an SO(10) model

In the context of non-supersymmetric SO(10) models, we analyze the renormalization group equations for the fermions (including neutrinos) from the GUT energy scale down to the electroweak energy scale, explicitly taking into account the effects of an intermediate energy scale induced by a Pati--Salam gauge group. To determine the renormalization group running, we use a numerical minimization procedure based on a nested sampling algorithm that randomly generates the values of 19 model parameters at the GUT scale, evolves them, and finally constructs the values of the physical observables and compares them to the existing experimental data at the electroweak scale. We show that the evolved fermion masses and mixings present sizable deviations from the values obtained without including the effects of the intermediate scale.Comment: Comments: 20 pages, 3 figures. Final version published in JHE