Mitochondrial pathogenic mutations are population-specific

<p>Abstract</p> <p>Background</p> <p>Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.</p> <p>Results</p> <p>We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.</p> <p>Conclusions</p> <p>Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.</p> <p>Reviewers</p> <p>This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).</p

Predicting Residential Air Exchange Rates from Questionnaires and Meteorology: Model Evaluation in Central North Carolina

A critical aspect of air pollution exposure models is the estimation of the air exchange rate (AER) of individual homes, where people spend most of their time. The AER, which is the airflow into and out of a building, is a primary mechanism for entry of outdoor air pollutants and removal of indoor source emissions. The mechanistic Lawrence Berkeley Laboratory (LBL) AER model was linked to a leakage area model to predict AER from questionnaires and meteorology. The LBL model was also extended to include natural ventilation (LBLX). Using literature-reported parameter values, AER predictions from LBL and LBLX models were compared to data from 642 daily AER measurements across 31 detached homes in central North Carolina, with corresponding questionnaires and meteorological observations. Data was collected on seven consecutive days during each of four consecutive seasons. For the individual model-predicted and measured AER, the median absolute difference was 43% (0.17 h−1) and 40% (0.17 h−1) for the LBL and LBLX models, respectively. Additionally, a literature-reported empirical scale factor (SF) AER model was evaluated, which showed a median absolute difference of 50% (0.25 h−1). The capability of the LBL, LBLX, and SF models could help reduce the AER uncertainty in air pollution exposure models used to develop exposure metrics for health studies

Valuing the risk associated with willow and miscanthus relative to conventional agricultural systems

The agronomic characteristics of willow and miscanthus make these crops highly susceptible to risk. This is particularly true in a country such as Ireland which has limited experience in the production of these crops. Issues such as soil and climate suitability have as yet to be resolved. The lengthy production lifespan of energy crops only serve to heighten the level of risk that affects key variables. The uncertainty surrounding the risk variables involved in producing willow and miscanthus, such as the annual yield level and the energy price, make it difficult to accurately calculate the returns of such a project. The returns from willow and miscanthus are compared with those of conventional agricultural enterprises using Stochastic Efficiency with Respect to a Function (SERF). A risk premium is calculated which farmers would need to be compensated with in order for them to be indifferent between their current enterprise and switching to biomass crop production. With the exception of spring barley, a risk premium is required if farmers are to be indifferent between their current enterprise and willow or miscanthus. The value of the risk premium required to entice farmers to switch to miscanthus production is significantly less than that required for willow. This suggests that a greater level of risk is associated with willow than with miscanthus.Biomass, SERF, Risk Premium, Resource /Energy Economics and Policy, Risk and Uncertainty,

Goal-Focused Emotion-Regulation Therapy (GET) for young adult survivors of testicular cancer: a pilot randomized controlled trial of a biobehavioral intervention protocol.

BackgroundTesticular cancer diagnosis and treatment, especially given its threat to sexuality and reproductive health, can be distressing in the formative period of young adulthood and the majority of young survivors experience impairing, distressing, and modifiable adverse outcomes that can persist long after medical treatment. These include psychological distress, impairment in pursuit of life goals, persistent physical side effects, elevated risk of secondary malignancies and chronic illness, and biobehavioral burden (e.g., enhanced inflammation, dysregulated diurnal stress hormones). However, few targeted interventions exist to assist young survivors in renegotiating life goals and regulating cancer-related emotions, and none focus on reducing the burden of morbidity via biobehavioral mechanisms. This paper describes the methodology of a randomized controlled biobehavioral trial designed to investigate the feasibility and preliminary impact of a novel intervention, Goal-focused Emotion-Regulation Therapy (GET), aimed at improving distress symptoms, emotion regulation, goal navigation skills, and stress-sensitive biomarkers in young adult testicular cancer patients.MethodsParticipants will be randomized to receive six sessions of GET or Individual Supportive Therapy (ISP) delivered over 8 weeks. In addition to indicators of intervention feasibility, we will measure primary (depressive and anxiety symptoms) and secondary (emotion regulation and goal navigation skills, career confusion) psychological outcomes prior to (T0), immediately after (T1), and 12 weeks after (T2) intervention. Additionally, identified biomarkers will be measured at baseline and at T2.DiscussionGET may have the potential to improve self-regulation across biobehavioral domains, improve overall cancer adjustment, and address the need for targeted supportive care interventions for young adult cancer survivors.Trial registrationClinicaltrials.gov, NCT04150848. Registered on 28 October 2019

Ultrasmooth gold surfaces prepared by chemical mechanical polishing for applications in nanoscience

For over 20 years, template stripping has been the best method for preparing ultrasmooth metal surfaces for studies of nanostructures. However, the organic adhesives used in the template stripping method are incompatible with many solvents, limiting the conditions that may subsequently be used to prepare samples; in addition, the film areas that can be reliably prepared are typically limited to ∼1 cm2. In this article, we present chemical-mechanical polishing (CMP) as an adhesive-free, scalable method of preparing ultrasmooth gold surfaces. In this process, a gold film is first deposited by e-beam evaporation onto a 76-mm-diameter silicon wafer. The CMP process removes ∼4 nm of gold from the tops of the grains comprising the gold film to produce an ultrasmooth gold surface supported on the silicon wafer. We measured root-mean-square (RMS) roughness values using atomic force microscopy of 12 randomly sampled 1 μm × 1 μm areas on the surface of the wafer and repeated the process on 5 different CMP wafers. The average RMS roughness was 3.8 ± 0.5 Å, which is comparable to measured values for template-stripped gold (3.7 ± 0.5 Å). We also compared the use of CMP and template-stripped gold as bottom electrical contacts in molecular electronic junctions formed from n-alkanethiolate self-assembled monolayers as a sensitive test bed to detect differences in the topography of the gold surfaces. We demonstrate that these substrates produce statistically indistinguishable values for the tunneling decay coefficient β, which is highly sensitive to the gold surface topography

Rheumatoid leptomeningitis presenting with an acute neuropsychiatric disorder

Leptomeningitis is a rare central nervous system manifestation of rheumatoid arthritis, generally in patients with established chronic rheumatoid disease. We report a 41-year-old man without previous rheumatoid arthritis or psychiatric disorder who presented with an acute neuropsychiatric disturbance and polyarthralgia. His MR scan of brain showed asymmetric bifrontal leptomeningitis, confirmed on (18F)-fluoro-D-glucose-positron emission tomography. Other investigations showed highly positive serum and cerebrospinal fluid anti-cyclic citrullinated peptide. A leptomeningeal biopsy showed necrotising leptomeningeal inflammation with ill-defined granulomas and lymphoplasmacytic infiltrate without organisms. Prolonged high-dose corticosteroids and then rituximab resulted in recovery. Chronic leptomeningitis can present with an acute neuropsychiatric disorder. We highlight that early rheumatoid disease can, rarely, cause a chronic leptomeningitis, reversible with immunotherapy

Temporal proteomic profiling of postnatal human cortical development.

Healthy cortical development depends on precise regulation of transcription and translation. However, the dynamics of how proteins are expressed, function and interact across postnatal human cortical development remain poorly understood. We surveyed the proteomic landscape of 69 dorsolateral prefrontal cortex samples across seven stages of postnatal life and integrated these data with paired transcriptome data. We detected 911 proteins by liquid chromatography-mass spectrometry, and 83 were significantly associated with postnatal age (FDR < 5%). Network analysis identified three modules of co-regulated proteins correlated with age, including two modules with increasing expression involved in gliogenesis and NADH metabolism and one neurogenesis-related module with decreasing expression throughout development. Integration with paired transcriptome data revealed that these age-related protein modules overlapped with RNA modules and displayed collinear developmental trajectories. Importantly, RNA expression profiles that are dynamically regulated throughout cortical development display tighter correlations with their respective translated protein expression compared to those RNA profiles that are not. Moreover, the correspondence between RNA and protein expression significantly decreases as a function of cortical aging, especially for genes involved in myelination and cytoskeleton organization. Finally, we used this data resource to elucidate the functional impact of genetic risk loci for intellectual disability, converging on gliogenesis, myelination and ATP-metabolism modules in the proteome and transcriptome. We share all data in an interactive, searchable companion website. Collectively, our findings reveal dynamic aspects of protein regulation and provide new insights into brain development, maturation, and disease

Odd-even effects in charge transport across n-alkanethiolate-based SAMs

This paper compares rates of charge transport across self-assembled monolayers (SAMs) of n-alkanethiolates having odd and even numbers of carbon atoms (nodd and neven) using junctions with the structure MTS/SAM//Ga2O3/EGaIn (M = Au or Ag). Measurements of current density, J(V), across SAMs of n-alkanethiolates on AuTS and AgTS demonstrated a statistically significant odd-even effect on AuTS, but not on AgTS, that could be detected using this technique. Statistical analysis showed the values of tunneling current density across SAMs of n-alkanethiolates on AuTS with nodd and neven belonging to two separate sets, and while there is a significant difference between the values of injection current density, J0, for these two series (log|J0Au,even| = 4.0 ± 0.3 and log|J0Au,odd| = 4.5 ± 0.3), the values of tunneling decay constant, β, for nodd and neven alkyl chains are indistinguishable (βAu,even = 0.73 ± 0.02 Å-1, and βAu,odd= 0.74 ± 0.02 Å-1). A comparison of electrical characteristics across junctions of n-alkanethiolate SAMs on gold and silver electrodes yields indistinguishable values of β and J0 and indicates that a change that substantially alters the tilt angle of the alkyl chain (and, therefore, the thickness of the SAM) has no influence on the injection current density across SAMs of n-alkanethiolates

A Feasibility Study of Quantifying Longitudinal Brain Changes in Herpes Simplex Virus (HSV) Encephalitis Using Magnetic Resonance Imaging (MRI) and Stereology.

OBJECTIVES: To assess whether it is feasible to quantify acute change in temporal lobe volume and total oedema volumes in herpes simplex virus (HSV) encephalitis as a preliminary to a trial of corticosteroid therapy. METHODS: The study analysed serially acquired magnetic resonance images (MRI), of patients with acute HSV encephalitis who had neuroimaging repeated within four weeks of the first scan. We performed volumetric measurements of the left and right temporal lobes and of cerebral oedema visible on T2 weighted Fluid Attenuated Inversion Recovery (FLAIR) images using stereology in conjunction with point counting. RESULTS: Temporal lobe volumes increased on average by 1.6% (standard deviation (SD 11%) in five patients who had not received corticosteroid therapy and decreased in two patients who had received corticosteroids by 8.5%. FLAIR hyperintensity volumes increased by 9% in patients not receiving treatment with corticosteroids and decreased by 29% in the two patients that had received corticosteroids. CONCLUSIONS: This study has shown it is feasible to quantify acute change in temporal lobe and total oedema volumes in HSV encephalitis and suggests a potential resolution of swelling in response to corticosteroid therapy. These techniques could be used as part of a randomized control trial to investigate the efficacy of corticosteroids for treating HSV encephalitis in conjunction with assessing clinical outcomes and could be of potential value in helping to predict the clinical outcomes of patients with HSV encephalitis