Blood-based Transcriptomic and Proteomic Biomarkers of Emphysema.

Rationale: Emphysema is a chronic obstructive pulmonary disease phenotype with important prognostic implications. Identifying blood-based biomarkers of emphysema will facilitate early diagnosis and development of targeted therapies. Objectives: To discover blood omics biomarkers for chest computed tomography-quantified emphysema and develop predictive biomarker panels. Methods: Emphysema blood biomarker discovery was performed using differential gene expression, alternative splicing, and protein association analyses in a training sample of 2,370 COPDGene participants with available blood RNA sequencing, plasma proteomics, and clinical data. Internal validation was conducted in a COPDGene testing sample (n = 1,016), and external validation was done in the ECLIPSE study (n = 526). Because low body mass index (BMI) and emphysema often co-occur, we performed a mediation analysis to quantify the effect of BMI on gene and protein associations with emphysema. Elastic net models with bootstrapping were also developed in the training sample sequentially using clinical, blood cell proportions, RNA-sequencing, and proteomic biomarkers to predict quantitative emphysema. Model accuracy was assessed by the area under the receiver operating characteristic curves for subjects stratified into tertiles of emphysema severity. Measurements and Main Results: Totals of 3,829 genes, 942 isoforms, 260 exons, and 714 proteins were significantly associated with emphysema (false discovery rate, 5%) and yielded 11 biological pathways. Seventy-four percent of these genes and 62% of these proteins showed mediation by BMI. Our prediction models demonstrated reasonable predictive performance in both COPDGene and ECLIPSE. The highest-performing model used clinical, blood cell, and protein data (area under the receiver operating characteristic curve in COPDGene testing, 0.90; 95% confidence interval, 0.85-0.90). Conclusions: Blood transcriptome and proteome-wide analyses revealed key biological pathways of emphysema and enhanced the prediction of emphysema.

Lung Transcriptomics Links Emphysema to Barrier Dysfunction and Macrophage Subpopulations.

RATIONALE: While many studies have examined gene expression in lung tissue, the gene regulatory processes underlying emphysema are still not well understood. Finding efficient non-imaging screening methods and disease-modifying therapies has been challenging, but knowledge of the transcriptomic features of emphysema may help in this effort. OBJECTIVES: Our goals were to identify emphysema-associated biological pathways through transcriptomic analysis of bulk lung tissue, to determine the lung cell types in which these emphysema-associated pathways are altered, and to detect unique and overlapping transcriptomic signatures in blood and lung samples. METHODS: Using RNA-sequencing data from 446 samples in the Lung Tissue Research Consortium (LTRC) and 3,606 blood samples from the COPDGene study, we examined the transcriptomic features of chest computed tomography-quantified emphysema. We also leveraged publicly available lung single-cell RNA-sequencing data to identify cell types showing COPD-associated differential expression of the emphysema pathways found in the bulk analyses. MEASUREMENTS AND MAIN RESULTS: In the bulk lung RNA-seq analysis, 1,087 differentially expressed genes and 34 dysregulated pathways were significantly associated with emphysema. We observed alternative splicing of several genes and increased activity in pluripotency and cell barrier function pathways. Lung tissue and blood samples shared differentially expressed genes and biological pathways. Multiple lung cell types displayed dysregulation of epithelial barrier function pathways, and distinct pathway activities were observed among various macrophage subpopulations. CONCLUSIONS: This study identified emphysema-related changes in gene expression and alternative splicing, cell-type specific dysregulated pathways, and instances of shared pathway dysregulation between blood and lung.

Horizontal Chemistry.

In 1976 Raymond Williams commented, 'Culture is one of the two or three most complicated words in the English language.' Such implied difficulty has not prevented Bloomsbury Academic, since the 2000s, from publishing around forty series of their well-produced and generously illustrated Cultural Histories, with, according to their website, a further fifty in progress. Each series contains six volumes, each book covering, in theory, the same chronological period (antiquity, the Middle Ages, the Renaissance, the Enlightenment, the age of empire and the modern age), though there is some variation depending on precise topic. The idea is that one can use these books not only to read 'horizontally' about a subject across time, but also 'vertically' through different subjects in the same period - a idea made easier by the e-texts of the series on Bloomsbury's website.

Recommendation for validation and quality assurance of non-invasive prenatal testing for foetal blood groups and implications for IVD risk classification according to EU regulations.

BACKGROUND AND OBJECTIVES: Non-invasive assays for predicting foetal blood group status in pregnancy serve as valuable clinical tools in the management of pregnancies at risk of detrimental consequences due to blood group antigen incompatibility. To secure clinical applicability, assays for non-invasive prenatal testing of foetal blood groups need to follow strict rules for validation and quality assurance. Here, we present a multi-national position paper with specific recommendations for validation and quality assurance for such assays and discuss their risk classification according to EU regulations. MATERIALS AND METHODS: We reviewed the literature covering validation for in-vitro diagnostic (IVD) assays in general and for non-invasive foetal RHD genotyping in particular. Recommendations were based on the result of discussions between co-authors. RESULTS: In relation to Annex VIII of the In-Vitro-Diagnostic Medical Device Regulation 2017/746 of the European Parliament and the Council, assays for non-invasive prenatal testing of foetal blood groups are risk class D devices. In our opinion, screening for targeted anti-D prophylaxis for non-immunized RhD negative women should be placed under risk class C. To ensure high quality of non-invasive foetal blood group assays within and beyond the European Union, we present specific recommendations for validation and quality assurance in terms of analytical detection limit, range and linearity, precision, robustness, pre-analytics and use of controls in routine testing. With respect to immunized women, different requirements for validation and IVD risk classification are discussed. CONCLUSION: These recommendations should be followed to ensure appropriate assay performance and applicability for clinical use of both commercial and in-house assays.

Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation.

Cigarette smoking induces a profound transcriptomic and systemic inflammatory response. Previous studies have focused on gene level differential expression of smoking, but the genome-wide effects of smoking on alternative isoform regulation have not yet been described. We conducted RNA sequencing in whole-blood samples of 454 current and 767 former smokers in the COPDGene Study, and we analyzed the effects of smoking on differential usage of isoforms and exons. At 10% FDR, we detected 3167 differentially expressed genes, 945 differentially used isoforms and 160 differentially used exons. Isoform switch analysis revealed widespread 3' UTR lengthening associated with cigarette smoking. The lengthening of these 3' UTRs was consistent with alternative usage of distal polyadenylation sites, and these extended 3' UTR regions were significantly enriched with functional sequence elements including microRNA and RNA-protein binding sites. These findings warrant further studies on alternative polyadenylation events as potential biomarkers and novel therapeutic targets for smoking-related diseases.

Comments on "Investigation of Histology Region Dielectric Measurements of Heterogeneous Tissues".

In the paper, "Investigation of histology region in dielectric measurements of heterogeneous tissues," by Porter and O'Halloran, the authors utilize a flexible phantom in a layered material dielectric property analysis to quantify the effective sensing volume of a coaxial dielectric probe. Ostensibly, this test has been used by others to characterize the region for which percent variation in the material composition in front of the probe corresponds to percent variation in the computed effective dielectric properties. By employing a compressible material, the authors fail to isolate features that are attributable solely to the probe, itself, and inadvertently incorporate confounding characteristics associated with the compressible nature of the material. The net effect is to exaggerate the probe's sensing volume which undermines conclusions drawn from the subsequent tissue dielectric property studies.

Validation of a Broadband Tissue-Equivalent Liquid for SAR Measurement and Monitoring of Its Dielectric Properties for Use in a Sealed Phantom.

We report on the development of a method for measuring the permittivity and conductivity of fluids inside a sealed tank (or a pipe) by using an embedded coaxial probe. Permittivity and conductivity in the frequency range 600 MHz to 6 GHz are determined from measurements of a complex reflection coefficient by using a vector network analyser (VNA) that is connected to the embedded probe via a coaxial cable. Substitution methods for calibration of an inaccessible probe are studied in this paper. These require the VNA with attached cable to be calibrated prior to connecting the cable to the embedded coaxial probe. Measurement of permittivity and conductivity of fluids inside sealed tanks and pipes is needed for monitoring industrial processes, such as fermentation. The authors' requirement, however, was to allow monitoring of a tissue-equivalent liquid that is contained inside a sealed tank. This tank is a component of a commercial system for rapid, multiple-band measurement of the specific absorption rate (SAR) of mobile phone handsets. Monitoring of permittivity and conductivity is needed to ensure compliance with international standards for SAR measurement. The paper also presents data for a new broadband (600 MHz to 6 GHz) tissue-equivalent liquid that is based on an oil-in-water emulsion. It is demonstrated that over an extended period of time, the liquid is stable, and an embedded coaxial probe enables its properties to be monitored with the required accuracy.

Unique aspects of peripheral artery disease in patients with chronic kidney disease.

Peripheral artery disease (PAD) represents a major health care burden. Despite the advent of screening and interventional procedures, the long-term clinical outcomes remain suboptimal, especially in patients with chronic kidney disease (CKD). While CKD and PAD share common predisposing factors, emerging studies indicate that their co-existence is not merely an association; instead, CKD represents a strong, independent risk factor for PAD. These findings implicate CKD-specific mediators of PAD that remain incompletely understood. Moreover, there is a need to understand the mechanisms underlying poor outcomes after interventions for PAD in CKD. This review discusses unique clinical aspects of PAD in patients with CKD, including high prevalence and worse outcomes after vascular interventions and the influence of renal allograft transplantation. In doing so, it also highlights underappreciated aspects of PAD in patients with CKD, such as disparities in revascularization and higher peri-procedural mortality. While previous reviews have discussed general mechanisms of PAD pathogenesis, focusing on PAD in CKD, this review underscores a need to probe for CKD-specific pathogenic pathways that may unravel novel biomarkers and therapeutic targets in PAD and ultimately improve the risk stratification and management of patients with CKD and PAD.

Effects of Selective Substitution of Cysteine Residues on the Conformational Properties of Chlorotoxin Explored by Molecular Dynamics Simulations.

Chlorotoxin (CTX) is a 36⁻amino acid peptide with eight Cys residues that forms four disulfide bonds. It has high affinity for the glioma-specific chloride channel and matrix metalloprotease-2. Structural and binding properties of CTX analogs with various Cys residue substitutions with l-α-aminobutyric acid (Abu) have been previously reported. Using 4.2 µs molecular dynamics, we compared the conformational and essential space sampling of CTX and analogs with selective substitution of the Cys residues and associated disulfide bonds with either Abu or Ser. The native and substituted peptides maintained a high degree of α-helix propensity from residues 8 through 21, with the exception of substitution of the Cys5⁻Cys28 residues with Ser and the Cys16⁻Cys33 residues with Abu. In agreement with previous circular dichroism spectropolarimetry results, the C-terminal ß-sheet content varied less from residues 25 through 29 and 32 through 36 and was well conserved in most analogs. The Cys16⁻Cys33 and Cys20⁻Cys35 disulfide-bonded residues appear to be required to maintain the αß motif of CTX. Selective substitution with the hydrophilic Ser, may mitigate the destabilizing effect of Cys16⁻Cys33 substitution through the formation of an inter residue H-bond from Ser16:OγH to Ser33:OγH bridged by a water molecule. All peptides shared considerable sampled conformational space, which explains the retained receptor binding of the non-native analogs.

Effects of force fields on the conformational and dynamic properties of amyloid ß(1-40) dimer explored by replica exchange molecular dynamics simulations.

The conformational space and structural ensembles of amyloid beta (Aß) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aß(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of ß-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected ß-sheet-turn-ß-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.

Unique methionine-aromatic interactions govern the calmodulin redox sensor.

Calmodulin contains multiple redox sensitive methionines whose oxidation alters the regulation of numerous targets. Molecular dynamics simulations were used to define the molecular principles that govern how calmodulin is structurally poised to detect and respond to methionine oxidation. We found that calmodulin's open and closed states were preferentially stabilized by unique, redox sensitive, methionine-aromatic interactions. Key methionine-aromatic interactions were coupled to reorientation of EF hand helices. Methionine to glutamine substitutions designed to mimic methionine oxidation strongly altered conformational transitions by modulating the strength of methionine-aromatic interactions. Together, these results suggest a broadly applicable redox sensing mechanism though which methionine oxidation by cellular oxidants alters the strength of methionine-aromatic interactions critical for functional protein dynamics.

Structural properties of amyloid ß(1-40) dimer explored by replica exchange molecular dynamics simulations.

Replica exchange molecular dynamics simulations (300 ns) were used to study the dimerization of amyloid ß(1-40) (Aß(1-40)) polypeptide. Configurational entropy calculations revealed that at physiological temperature (310 K, 37°C) dynamic dimers are formed by randomly docked monomers. Free energy of binding of the two chains to each other was -93.56 ± 6.341 kJ mol-1 . Prevalence of random coil conformations was found for both chains with the exceptions of increased ß-sheet content from residues 16-21 and 29-32 of chain A and residues 15-21 and 30-33 of chain B with ß-turn/ß-bend conformations in both chains from residues 1-16, 21-29 of chain A, 1-16, and 21-29 of chain B. There is a mixed ß-turn/ß-sheet region from residues 33-38 of both chains. Analysis of intra- and interchain residue distances shows that, although the individual chains are highly flexible, the dimer system stays in a loosely packed antiparallel ß-sheet configuration with contacts between residues 17-21 of chain A with residues 17-21 and 31-36 of chain B as well as residues 31-36 of chain A with residues 17-21 and 31-36 of chain B. Based on dihedral principal component analysis, the antiparallel ß-sheet-loop-ß-sheet conformational motif is favored for many low energy sampled conformations. Our results show that Aß(1-40) can form dynamic dimers in aqueous solution that have significant conformational flexibility and are stabilized by collapse of the central and C-terminal hydrophobic cores with the expected ß-sheet-loop-ß-sheet conformational motif. Proteins 2017; 85:1024-1045. © 2017 Wiley Periodicals, Inc.

The DAU cluster: a comparative analysis of 18 RHD alleles, some forming partial D antigens.

BACKGROUND: The Rh system is the most complex and polymorphic blood group system in humans with more than 460 alleles known for the RHD gene. The DAU cluster of RHD alleles is characterized by the single-nucleotide change producing the p.Thr379Met amino acid substitution. It is called the DAU-0 allele and has been postulated to be the primordial allele, from which all other alleles of the DAU cluster have eventually evolved. STUDY DESIGN AND METHODS: For two novel DAU alleles, the nucleotide sequences of all 10 exons as well as adjacent intronic regions, including the 5' and 3' untranslated regions (UTR), were determined for the RHD and RHCE genes. A phylogenetic tree for all DAU alleles was established using the neighbor-joining method with Pan troglodytes as root. Standard hemagglutination and flow cytometry tests were performed. RESULTS: We characterized two DAU alleles, DAU-11 and DAU-5.1, closely related to DAU-3 and DAU-5, respectively. A phylogenetic analysis of the 18 known DAU alleles indicated point mutations and interallelic recombination contributing to diversification of the DAU cluster. CONCLUSIONS: The DAU alleles encode a group of RhD protein variants, some forming partial D antigens known to permit anti-D in carriers; all are expected to cause anti-D alloimmunization in recipients of red blood cell transfusions. The DAU alleles evolved through genomic point mutations and recombination. These results suggest that the cluster of DAU alleles represent a clade, which is concordant with our previous postulate that they derived from the primordial DAU-0 allele.

Open-Ended Coaxial Dielectric Probe Effective Penetration Depth Determination.

We have performed a series of experiments which demonstrate the effect of open-ended coaxial diameter on the depth of penetration. We used a two layer configuration of a liquid and movable cylindrical piece of either Teflon or acrylic. The technique accurately demonstrates the depth in a sample for which a given probe diameter provides a reasonable measure of the bulk dielectric properties for a heterogeneous volume. In addition we have developed a technique for determining the effective depth for a given probe diameter size. Using a set of simulations mimicking four 50 Ω coaxial cable diameters, we demonstrate that the penetration depth in both water and saline has a clear dependence on probe diameter but is remarkably uniform over frequency and with respect to the intervening liquid permittivity. Two different 50 Ω commercial probes were similarly tested and confirm these observations. This result has significant implications to a range of dielectric measurements, most notably in the area of tissue property studies.

Call to Action on Making Physical Activity Assessment and Prescription a Medical Standard of Care.

The U.S. population is plagued by physical inactivity, lack of cardiorespiratory fitness, and sedentary lifestyles, all of which are strongly associated with the emerging epidemic of chronic disease. The time is right to incorporate physical activity assessment and promotion into health care in a manner that engages clinicians and patients. In April 2015, the American College of Sports Medicine and Kaiser Permanente convened a joint consensus meeting of subject matter experts from stakeholder organizations to discuss the development and implementation of a physical activity vital sign (PAVS) to be obtained and recorded at every medical visit for every patient. This statement represents a summary of the discussion, recommendations, and next steps developed during the consensus meeting. Foremost, it is a "call to action" for current and future clinicians and the health care community to implement a PAVS in daily practice with every patient.

Isotope fractionation factors controlling isotopocule signatures of soil-emitted N2O produced by denitrification processes of various rates.

RATIONALE: This study aimed (i) to determine the isotopic fractionation factors associated with N2O production and reduction during soil denitrification and (ii) to help specify the factors controlling the magnitude of the isotope effects. For the first time the isotope effects of denitrification were determined in an experiment under oxic atmosphere and using a novel approach where N2O production and reduction occurred simultaneously. METHODS: Soil incubations were performed under a He/O2 atmosphere and the denitrification product ratio [N2O/(N2 + N2O)] was determined by direct measurement of N2 and N2O fluxes. N2O isotopocules were analyzed by mass spectrometry to determine δ(18)O, δ(15)N and (15)N site preference within the linear N2O molecule (SP). An isotopic model was applied for the simultaneous determination of net isotope effects (η) of both N2O production and reduction, taking into account emissions from two distinct soil pools. RESULTS: A clear relationship was observed between (15)N and (18)O isotope effects during N2O production and denitrification rates. For N2O reduction, diverse isotope effects were observed for the two distinct soil pools characterized by different product ratios. For moderate product ratios (from 0.1 to 1.0) the range of isotope effects given by previous studies was confirmed and refined, whereas for very low product ratios (below 0.1) the net isotope effects were much smaller. CONCLUSIONS: The fractionation factors associated with denitrification, determined under oxic incubation, are similar to the factors previously determined under anoxic conditions, hence potentially applicable for field studies. However, it was shown that the η(18)O/η(15)N ratios, previously accepted as typical for N2O reduction processes (i.e., higher than 2), are not valid for all conditions.

High yielding biomass genotypes of willow (Salix spp.) show differences in below ground biomass allocation.

Willows (Salix spp.) grown as short rotation coppice (SRC) are viewed as a sustainable source of biomass with a positive greenhouse gas (GHG) balance due to their potential to fix and accumulate carbon (C) below ground. However, exploiting this potential has been limited by the paucity of data available on below ground biomass allocation and the extent to which it varies between genotypes. Furthermore, it is likely that allocation can be altered considerably by environment. To investigate the role of genotype and environment on allocation, four willow genotypes were grown at two replicated field sites in southeast England and west Wales, UK. Above and below ground biomass was intensively measured over two two-year rotations. Significant genotypic differences in biomass allocation were identified, with below ground allocation differing by up to 10% between genotypes. Importantly, the genotype with the highest below ground biomass also had the highest above ground yield. Furthermore, leaf area was found to be a good predictor of below ground biomass. Growth environment significantly impacted allocation; the willow genotypes grown in west Wales had up to 94% more biomass below ground by the end of the second rotation. A single investigation into fine roots showed the same pattern with double the volume of fine roots present. This greater below ground allocation may be attributed primarily to higher wind speeds, plus differences in humidity and soil characteristics. These results demonstrate that the capacity exists to breed plants with both high yields and high potential for C accumulation.

Response variables for evaluation of the effectiveness of conservation corridors.

Many studies have evaluated effectiveness of corridors by measuring species presence in and movement through small structural corridors. However, few studies have assessed whether these response variables are adequate for assessing whether the conservation goals of the corridors have been achieved or considered the costs or lag times involved in measuring the response variables. We examined 4 response variables-presence of the focal species in the corridor, interpatch movement via the corridor, gene flow, and patch occupancy--with respect to 3 criteria--relevance to conservation goals, lag time (fewest generations at which a positive response to the corridor might be evident with a particular variable), and the cost of a study when applying a particular variable. The presence variable had the least relevance to conservation goals, no lag time advantage compared with interpatch movement, and only a moderate cost advantage over interpatch movement or gene flow. Movement of individual animals between patches was the most appropriate response variable for a corridor intended to provide seasonal migration, but it was not an appropriate response variable for corridor dwellers, and for passage species it was only moderately relevant to the goals of gene flow, demographic rescue, and recolonization. Response variables related to gene flow provided a good trade-off among cost, relevance to conservation goals, and lag time. Nonetheless, the lag time of 10-20 generations means that evaluation of conservation corridors cannot occur until a few decades after a corridor has been established. Response variables related to occupancy were most relevant to conservation goals, but the lag time and costs to detect corridor effects on occupancy were much greater than the lag time and costs to detect corridor effects on gene flow.

Effects of wind energy development on nesting ecology of greater prairie-chickens in fragmented grasslands.

Wind energy is targeted to meet 20% of U.S. energy needs by 2030, but new sites for development of renewable energy may overlap with important habitats of declining populations of grassland birds. Greater Prairie-Chickens (Tympanuchus cupido) are an obligate grassland bird species predicted to respond negatively to energy development. We used a modified before-after control-impact design to test for impacts of a wind energy development on the reproductive ecology of prairie-chickens in a 5-year study. We located 59 and 185 nests before and after development, respectively, of a 201 MW wind energy facility in Greater Prairie-Chicken nesting habitat and assessed nest site selection and nest survival relative to proximity to wind energy infrastructure and habitat conditions. Proximity to turbines did not negatively affect nest site selection (ß = 0.03, 95% CI = -1.2-1.3) or nest survival (ß = -0.3, 95% CI = -0.6-0.1). Instead, nest site selection and survival were strongly related to vegetative cover and other local conditions determined by management for cattle production. Integration of our project results with previous reports of behavioral avoidance of oil and gas facilities by other species of prairie grouse suggests new avenues for research to mitigate impacts of energy development.