Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements

Retinitis pigmentosa (RP) is a devastating form of retinal degeneration, with significant social and professional consequences. Molecular genetic information is invaluable for an accurate clinical diagnosis of RP due to its high genetic and clinical heterogeneity. Using a gene capture panel that covers 163 of the currently known retinal disease genes, including 48 RP genes, we performed a comprehensive molecular screening in a collection of 123 RP unsettled probands from a wide variety of ethnic backgrounds, including 113 unrelated simplex and 10 autosomal recessive RP (arRP) cases. As a result, 61 mutations were identified in 45 probands, including 38 novel pathogenic alleles. Interestingly, we observed that phenotype and genotype were not in full agreement in 21 probands. Among them, eight probands were clinically reassessed, resulting in refinement of clinical diagnoses for six of these patients. Finally, recessive mutations in CLN3 were identified in five retinal degeneration patients, including four RP probands and one cone-rod dystrophy patient, suggesting that CLN3 is a novel non-syndromic retinal disease gene. Collectively, our results underscore that, due to the high molecular and clinical heterogeneity of RP, comprehensive screening of all retinal disease genes is effective in identifying novel pathogenic mutations and provides an opportunity to discover new genotype-phenotype correlations. Information gained from this genetic screening will directly aid in patient diagnosis, prognosis, and treatment, as well as allowing appropriate family planning and counseling.

Whole-Vehicle modelling of exhaust energy recovery on a diesel-electric hybrid bus

Hybrid vehicles can use energy storage systems to disconnect the engine from the driving wheels of the vehicle. This enables the engine to be run closer to its optimum operating condition, but fuel energy is still wasted through the exhaust system as heat. The use of a turbogenerator on the exhaust line addresses this problem by capturing some of the otherwise wasted heat and converting it into useful electrical energy.

This paper outlines the work undertaken to model the engine of a diesel-electric hybrid bus, coupled with a hybrid powertrain model which analysed the performance of a hybrid vehicle over a drive-cycle. The distribution of the turbogenerator power was analysed along with the effect on the fuel consumption of the bus. This showed that including the turbogenerator produced a 2.4% reduction in fuel consumption over a typical drive-cycle.

The hybrid bus generator was then optimised to improve the performance of the combined vehicle/engine package and the turbogenerator was then shown to offer a 3.0% reduction in fuel consumption. The financial benefits of using the turbogenerator were also considered in terms of fuel savings for operators. For an average bus, a turbogenerator could reduce fuel costs by around £1200 per year.

Integrating allowable design strains in composites with whole life value

Fibre-Reinforced Plastics (FRPs) have been used in civil aerospace vehicles for decades. The current state-of-the-art in airframe design and manufacture results in approximately half the airframe mass attributable to FRP materials. The continual increase in the use of FRP materials over metallic alloys is attributable to the material's superior specific strength and stiffness, fatigue performance and corrosion resistance. However, the full potential of these materials has yet to be exploited as analysis methods to predict physical failure with equal accuracy and robustness are not yet available. The result is a conservative approach to design, but one that can bring benefit via increased inspection intervals and reduced cost over the vehicle life. The challenge is that the methods used in practice are based on empirical tests and real relationships and drivers are difficult to see in this complex process and so the trade-off decision is challenging and uncertain. The aim of this feasibility study was to scope a viable process which could help develop some rules and relationships based on the fundamental mechanics of composite material and the economics of production and operation, which would enhance understanding of the role and impact of design allowables across the life of a composite structure.

Enhancement of whole cell dioxygenase biotransformations of haloarenes by toxic ionic liquids

Accessing chirally pure cis-diols from arenes using micro-organisms over-expressing toluene dioxygenase (TDO) is now well established, but the conversions remain low for the more toxic and volatile substrates. For such arenes, improved production has already been achieved in the presence of hydrophobic non-toxic ionic liquids (ILs) acting in the form of a reservoir for the arene substrate. Yet, the costs associated with such ILs require extensive process development to render them viable. Herein, we show that optimization of the hydrophobic IL's cationic moiety and of the IL's concentration are key to enhanced conversion yielding between a 2-5 fold yield increase in the conversion of four haloarenes (Ph-X; X = F, Cl, Br, I). Additionally, we report that hydrophilic imidazolium-based ILs offer opportunities to achieve similarly high yielding biotransformations, with further improved reaction rates (<6 h), and this at very low ILs' concentrations (0.0015 V_IL/V_aq). We also demonstrate that the increased biotransformations are due to these ILs being inhibitors of cellular respiration processes and thus favoring the shunting of NADH and O₂ towards the overexpressed biocatalytic process. © 2014 the Partner Organisations.

Multi-Fidelity Multidisciplinary Whole Engine Thermo-Mechanical Design Optimization

Traditionally, the optimization of a turbomachinery engine casing for tip clearance has involved either twodimensional transient thermomechanical simulations or three-dimensional mechanical simulations. This paper illustrates that three-dimensional transient whole-engine thermomechanical simulations can be used within tip clearance optimizations and that the efficiency of such optimizations can be improved when a multifidelity surrogate modeling approach is employed. These simulations are employed in conjunction with a rotor suboptimization using surrogate models of rotor-dynamics performance, stress, mass and transient displacements, and an engine parameterization.

Laughter Type Recognition from Whole Body Motion

Despite the importance of laughter in social interactions it remains little studied in affective computing. Respiratory, auditory, and facial laughter signals have been investigated but laughter-related body movements have received almost no attention. The aim of this study is twofold: first an investigation into observers' perception of laughter states (hilarious, social, awkward, fake, and non-laughter) based on body movements alone, through their categorization of avatars animated with natural and acted motion capture data. Significant differences in torso and limb movements were found between animations perceived as containing laughter and those perceived as nonlaughter. Hilarious laughter also differed from social laughter in the amount of bending of the spine, the amount of shoulder rotation and the amount of hand movement. The body movement features indicative of laughter differed between sitting and standing avatar postures. Based on the positive findings in this perceptual study, the second aim is to investigate the possibility of automatically predicting the distributions of observer's ratings for the laughter states. The findings show that the automated laughter recognition rates approach human rating levels, with the Random Forest method yielding the best performance.

Next-generation sequencing of the mitochondrial genome and association with IgA nephropathy in a renal transplant population

Kidneys are highly aerobic organs that are critically dependent on the normal functioning of mitochondria. Genetic variations disrupting mitochondrial function are associated with multifactorial disorders including kidney disease. This study sequenced the entire mitochondrial genome in a renal transplant cohort of 64 individuals, using next-generation sequencing, to evaluate the association of genetic variants with IgA nephropathy and end-stage renal disease (ESRD, n = 100).

Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland

Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by progressive photoreceptor degeneration. An accurate molecular diagnosis is essential for disease characterization and clinical prognoses. A retinal capture panel that enriches 186 known retinal disease genes, including 55 known RP genes, was developed. Targeted next-generation sequencing was performed for a cohort of 82 unrelated RP cases from Northern Ireland, including 46 simplex cases and 36 familial cases. Disease-causing mutations were identified in 49 probands, including 28 simplex cases and 21 familial cases, achieving a solving rate of 60 %. In total, 65 pathogenic mutations were found, and 29 of these were novel. Interestingly, the molecular information of 12 probands was neither consistent with their initial inheritance pattern nor clinical diagnosis. Further clinical reassessment resulted in a refinement of the clinical diagnosis in 11 patients. This is the first study to apply next-generation sequencing-based, comprehensive molecular diagnoses to a large number of RP probands from Northern Ireland. Our study shows that molecular information can aid clinical diagnosis, potentially changing treatment options, current family counseling and management.

Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection

UNLABELLED: Burkholderia pseudomallei causes the potentially fatal disease melioidosis. It is generally accepted that B. pseudomallei is a noncommensal bacterium and that any culture-positive clinical specimen denotes disease requiring treatment. Over a 23-year study of melioidosis cases in Darwin, Australia, just one patient from 707 survivors has developed persistent asymptomatic B. pseudomallei carriage. To better understand the mechanisms behind this unique scenario, we performed whole-genome analysis of two strains isolated 139 months apart. During this period, B. pseudomallei underwent several adaptive changes. Of 23 point mutations, 78% were nonsynonymous and 43% were predicted to be deleterious to gene function, demonstrating a strong propensity for positive selection. Notably, a nonsense mutation inactivated the universal stress response sigma factor RpoS, with pleiotropic implications. The genome underwent substantial reduction, with four deletions in chromosome 2 resulting in the loss of 221 genes. The deleted loci included genes involved in secondary metabolism, environmental survival, and pathogenesis. Of 14 indels, 11 occurred in coding regions and 9 resulted in frameshift mutations that dramatically affected predicted gene products. Disproportionately, four indels affected lipopolysaccharide biosynthesis and modification. Finally, we identified a frameshift mutation in both P314 isolates within wcbR, an important component of the capsular polysaccharide I locus, suggesting virulence attenuation early in infection. Our study illustrates a unique clinical case that contrasts a high-consequence infectious agent with a long-term commensal infection and provides further insights into bacterial evolution within the human host.

IMPORTANCE: Some bacterial pathogens establish long-term infections that are difficult or impossible to eradicate with current treatments. Rapid advances in genome sequencing technologies provide a powerful tool for understanding bacterial persistence within the human host. Burkholderia pseudomallei is considered a highly pathogenic bacterium because infection is commonly fatal. Here, we document within-host evolution of B. pseudomallei in a unique case of human infection with ongoing chronic carriage. Genomic comparison of isolates obtained 139 months (11.5 years) apart showed a strong signal of adaptation within the human host, including inactivation of virulence and immunogenic factors, and deletion of pathways involved in environmental survival. Two global regulatory genes were mutated in the 139-month isolate, indicating extensive regulatory changes favoring bacterial persistence. Our study provides insights into B. pseudomallei pathogenesis and, more broadly, identifies parallel evolutionary mechanisms that underlie chronic persistence of all bacterial pathogens.

Next-generation sequencing: a change of paradigm in molecular diagnostic validation

Next-generation sequencing (NGS) is beginning to show its full potential for diagnostic and therapeutic applications. In particular, it is enunciating its capacity to contribute to a molecular taxonomy of cancer, to be used as a standard approach for diagnostic mutation detection, and to open new treatment options that are not exclusively organ-specific. If this is the case, how much validation is necessary and what should be the validation strategy, when bringing NGS into the diagnostic/clinical practice? This validation strategy should address key issues such as: what is the overall extent of the validation? Should essential indicators of test performance such as sensitivity of specificity be calculated for every target or sample type? Should bioinformatic interpretation approaches be validated with the same rigour? What is a competitive clinical turnaround time for a NGS-based test, and when does it become a cost-effective testing proposition? While we address these and other related topics in this commentary, we also suggest that a single set of international guidelines for the validation and use of NGS technology in routine diagnostics may allow us all to make a much more effective use of resources.

Perception and Automatic Recognition of Laughter from Whole-Body Motion: Continuous and Categorical Perspectives

Despite its importance in social interactions, laughter remains little studied in affective computing. Intelligent virtual agents are often blind to users’ laughter and unable to produce convincing laughter themselves. Respiratory, auditory, and facial laughter signals have been investigated but laughter-related body movements have received less attention. The aim of this study is threefold. First, to probe human laughter perception by analyzing patterns of categorisations of natural laughter animated on a minimal avatar. Results reveal that a low dimensional space can describe perception of laughter “types”. Second, to investigate observers’ perception of laughter (hilarious, social, awkward, fake, and non-laughter) based on animated avatars generated from natural and acted motion-capture data. Significant differences in torso and limb movements are found between animations perceived as laughter and those perceived as non-laughter. Hilarious laughter also differs from social laughter. Different body movement features were indicative of laughter in sitting and standing avatar postures. Third, to investigate automatic recognition of laughter to the same level of certainty as observers’ perceptions. Results show recognition rates of the Random Forest model approach human rating levels. Classification comparisons and feature importance analyses indicate an improvement in recognition of social laughter when localized features and nonlinear models are used.

Characterisation of a novel panel of polymorphic microsatellite loci for the liver fluke, Fasciola hepatica, using a next generation sequencing approach

The liver fluke, Fasciola hepatica is an economically important pathogen of sheep and cattle and has been described by the WHO as a re-emerging zoonosis. Control is heavily reliant on the use of drugs, particularly triclabendazole and as a result resistance has now emerged. The population structure of F. hepatica is not well known, yet it can impact on host-parasite interactions and parasite control with drugs, particularly regarding the spread of triclabendazole resistance. We have identified 2448 potential microsatellites from 83Mb of F. hepatica genome sequence using msatfinder. Thirty-five loci were developed and optimised for microsatellite PCR, resulting in a panel of 15 polymorphic loci, with a range of three to 15 alleles. This panel was validated on genomic DNA from 46 adult F. hepatica; 38 liver flukes sourced from a Northwest abattoir, UK and 8 liver flukes from an established isolate (Shrewsbury; Ridgeway Research). Evidence for null alleles was found at four loci (Fh_1, Fh_8, Fh_13 and Fh_14), which showed markedly higher levels of homozygosity than the remaining 11 loci. Of the 38 liver flukes isolated from cattle livers (n=10) at the abattoir, 37 genotypes were identified. Using a multiplex approach all 15 loci could be amplified from several life cycle stages that typically yield low amounts of DNA, including metacercariae, the infective life cycle stage present on pasture, highlighting the utility of this multiplex microsatellite panel. This study reports the largest panel of microsatellite markers available to date for population studies of F. hepatica and the first multiplex panel of microsatellite markers that can be used for several life cycle stages.