Complement Factor I Variants in Complement-Mediated Renal Diseases.

C3 glomerulopathy (C3G) and atypical hemolytic uremic syndrome (aHUS) are two rare diseases caused by dysregulated activity of the alternative pathway of complement secondary to the presence of genetic and/or acquired factors. Complement factor I (FI) is a serine protease that downregulates complement activity in the fluid phase and/or on cell surfaces in conjunction with one of its cofactors, factor H (FH), complement receptor 1 (CR1/CD35), C4 binding protein (C4BP) or membrane cofactor protein (MCP/CD46). Because altered FI activity is causally related to the pathogenesis of C3G and aHUS, we sought to test functional activity of select CFI missense variants in these two patient cohorts. We identified 65 patients (16, C3G; 48, aHUS; 1 with both) with at least one rare variant in CFI (defined as a MAF < 0.1%). Eight C3G and eleven aHUS patients also carried rare variants in either another complement gene, ADAMTS13 or THBD. We performed comprehensive complement analyses including biomarker profiling, pathway activity and autoantibody testing, and developed a novel FI functional assay, which we completed on 40 patients. Seventy-eight percent of rare CFI variants (31/40) were associated with FI protein levels below the 25th percentile; in 22 cases, FI levels were below the lower limit of normal (type 1 variants). Of the remaining nine variants, which associated with normal FI levels, two variants reduced FI activity (type 2 variants). No patients carried currently known autoantibodies (including FH autoantibodies and nephritic factors). We noted that while rare variants in CFI predispose to complement-mediated diseases, phenotypes are strongly contingent on the associated genetic background. As a general rule, in isolation, a rare CFI variant most frequently leads to aHUS, with the co-inheritance of a CD46 loss-of-function variant driving the onset of aHUS to the younger age group. In comparison, co-inheritance of a gain-of-function variant in C3 alters the phenotype to C3G. Defects in CFH (variants or fusion genes) are seen with both C3G and aHUS. This variability underscores the complexity and multifactorial nature of these two complement-mediated renal diseases.

Full Inversion Tillage (FIT) during pasture renewal as a potential management strategy for enhanced carbon sequestration and storage in Irish grassland soils.

It has been suggested that the sequestration of CO2 by agricultural soils offers a means to reduce atmospheric greenhouse gas (GHG) concentrations and in turn mitigate the impacts of climate change. Carbon sequestration by grassland soils, which account for more than 60% of agricultural land use in Ireland, could contribute to a successful net reduction of atmospheric GHG emissions in accordance with the COP21 Paris Agreement. However, current estimates of soil carbon sequestration are variable and it is likely that many permanent grasslands are close to saturation. A literature search shows that soil carbon sequestration is enhanced by a variety of different management strategies, although one option that has only been examined to date in New Zealand is full inversion tillage (FIT) during grassland renovation. FIT involves inverting topsoil, generally to depths of 30 cm, resulting in the movement of C-deficient subsoil to the surface and the burying of carbon-rich topsoil. In this review, we hypothesise that over the next ~30 years the new topsoil could incorporate large amounts of soil organic carbon (SOC) from the re-seeded sward vegetation and that the buried carbon will be retained. We assess the current capability of Irish grassland soils to sequester carbon and suggest a potential role of FIT during grassland renovation. An analysis of the distribution of grasslands in Ireland using the Land Parcel Identification System (LPIS) suggests that ~26% of Ireland's agricultural grasslands are suitable for FIT.

Regional Variation in Genetic Control of Atherosclerosis in Hyperlipidemic Mice.

Atherosclerosis is a polygenic disorder that often affects multiple arteries. Carotid arteries are common sites for evaluating subclinical atherosclerosis, and aortic root is the standard site for quantifying atherosclerosis in mice. We compared genetic control of atherosclerosis between the two sites in the same cohort derived from two phenotypically divergent Apoe-null (Apoe-/-) mouse strains. Female F2 mice were generated from C57BL/6 (B6) and C3H/He (C3H) Apoe-/- mice and fed 12 weeks of Western diet. Atherosclerotic lesions in carotid bifurcation and aortic root and plasma levels of fasting lipids and glucose were measured. 153 genetic markers across the genome were typed. All F2 mice developed aortic atherosclerosis, while 1/5 formed no or little carotid lesions. Genome-wide scans revealed 3 significant loci on chromosome (Chr) 1, Chr15, 6 suggestive loci for aortic atherosclerosis, 2 significant loci on Chr6, Chr12, and 6 suggestive loci for carotid atherosclerosis. Only 2 loci for aortic lesions showed colocalization with loci for carotid lesions. Carotid lesion sizes were moderately correlated with aortic lesion sizes (r = 0.303; P = 4.6E-6), but they showed slight or no association with plasma HDL, non-HDL cholesterol, triglyceride, or glucose levels among F2 mice. Bioinformatics analyses prioritized Cryge as a likely causal gene for Ath30, Cdh6 and Dnah5 as causal genes for Ath22 Our data demonstrate vascular site-specific effects of genetic factors on atherosclerosis in the same animals and highlight the need to extend studies of atherosclerosis to sites beyond aortas of mice.

Can biomass supply meet the demands of bioenergy with carbon capture and storage (BECCS)?

To reach the reduced carbon emission targets proposed by the Paris agreement, one of the widely proposed decarbonizing strategies, referred to as negative emissions technologies (NETs), is the production and combustion of bioenergy crops in conjunction with carbon capture and storage (BECCS). However, concerns have been increasingly raised that relying on the potential of BECCS to achieve negative emissions could result in delayed reductions in gross CO2 emissions, with consequent high risk of overshooting global temperature targets. We focus on two particular issues: the carbon efficiency and payback time of bioenergy use in BECCS and the potential constraints on the supply of bioenergy. The simplistic vision of BECCS is that 1 tonne of CO2 captured in the growth of biomass equates to 1 tonne of CO2 sequestered geologically, but this cannot be the case as CO2 is emitted by variable amounts during the lifecycle from crop establishment to sequestration below ground in geological formations. The deployment of BECCS is ultimately reliant on the availability of sufficient, sustainably sourced, biomass. The two most important factors determining this supply are land availability and land productivity. The upper bounds of the area estimates required correspond to more than the world's harvested land for cereal production. To achieve these estimates of biomass availability requires the rapid evolution of a multitude of technological, social, political and economic factors. Here, we question whether, because of the limited sustainable supply of biomass, BECCS should continue to be considered the dominant NET in IPCC and other scenarios achieving the Paris targets, or should it be deemed no longer fit for purpose?

Factor H Autoantibodies and Complement-Mediated Diseases.

Factor H (FH), a member of the regulators-of-complement-activation (RCA) family of proteins, circulates in human plasma at concentrations of 180-420 mg/L where it controls the alternative pathway (AP) of complement in the fluid phase and on cell surfaces. When the regulatory function of FH is impaired, complement-mediated tissue injury and inflammation occur, leading to diseases such as atypical hemolytic uremic syndrome (a thrombotic microangiopathy or TMA), C3 glomerulopathy (C3G) and monoclonal gammopathy of renal significance (MGRS). A pathophysiological cause of compromised FH function is the development of autoantibodies to various domains of the FH protein. FH autoantibodies (FHAAs) are identified in 10.9% of patients with aHUS, 3.2% of patients with C3G, and rarely in patients with MGRS. The phenotypic variability of FHAA-mediated disease reflects both the complexity of FH and the epitope specificity of FHAA for select regions of the native protein. In this paper, we have characterized FHAA epitopes in a large cohort of patients diagnosed with TMA, C3G or MGRS. We explore the epitopes recognized by FHAAs in these diseases and the association of FHAAs with the genetic deletion of both copies of the CFHR1 gene to show how these disease phenotypes are associated with this diverse spectrum of autoantibodies.

Genetic Analysis of 400 Patients Refines Understanding and Implicates a New Gene in Atypical Hemolytic Uremic Syndrome.

BACKGROUND: Genetic variation in complement genes is a predisposing factor for atypical hemolytic uremic syndrome (aHUS), a life-threatening thrombotic microangiopathy, however interpreting the effects of genetic variants is challenging and often ambiguous. METHODS: We analyzed 93 complement and coagulation genes in 400 patients with aHUS, using as controls 600 healthy individuals from Iowa and 63,345 non-Finnish European individuals from the Genome Aggregation Database. After adjusting for population stratification, we then applied the Fisher exact, modified Poisson exact, and optimal unified sequence kernel association tests to assess gene-based variant burden. We also applied a sliding-window analysis to define the frequency range over which variant burden was significant. RESULTS: We found that patients with aHUS are enriched for ultrarare coding variants in the CFH, C3, CD46, CFI, DGKE, and VTN genes. The majority of the significance is contributed by variants with a minor allele frequency of <0.1%. Disease-related variants tend to occur in specific complement protein domains of FH, CD46, and C3. We observed no enrichment for multiple rare coding variants in gene-gene combinations. CONCLUSIONS: In known aHUS-associated genes, variants with a minor allele frequency >0.1% should not be considered pathogenic unless valid enrichment and/or functional evidence are available. VTN, which encodes vitronectin, an inhibitor of the terminal complement pathway, is implicated as a novel aHUS-associated gene. Patients with aHUS are not enriched for multiple rare variants in complement genes. In aggregate, these data may help in directing clinical management of aHUS.

Contaminants of emerging concern affect Trichoplusia ni growth and development on artificial diets and a key host plant.

Many countries are utilizing reclaimed wastewater for agriculture because drought, rising temperatures, and expanding human populations are increasing water demands. Unfortunately, wastewater often contains biologically active, pseudopersistent pharmaceuticals, even after treatment. Runoff from farms and output from wastewater treatment plants also contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on an agricultural pest, Trichoplusia ni (Lepidoptera: Noctuidae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Trichoplusia ni showed increased developmental time and mortality when reared on artificial diets containing antibiotics, hormones, or a mixture of contaminants. Mortality was also increased when T. ni were reared on tomatoes grown hydroponically with the same concentrations of antibiotics. The antibiotic-treated plants translocated ciprofloxacin through their tissues to roots, shoots, and leaves. Microbial communities of T. ni changed substantially between developmental stages and when exposed to CECs in their diets. Our results suggest that use of reclaimed wastewater for irrigation of crops can affect the developmental biology and microbial communities of an insect of agricultural importance.

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community.

Drought, rising temperatures, and expanding human populations are increasing water demands. Many countries are extending potable water supplies by irrigating crops with wastewater. Unfortunately, wastewater contains biologically active, long-lived pharmaceuticals, even after treatment. Run-off from farms and wastewater treatment plant overflows contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on a cosmopolitan saprophagous insect, Megaselia scalaris (Diptera: Phoridae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Female flies showed no oviposition preference for treated or untreated diets. Larvae exposed to caffeine in diets showed increased mortality, and larvae fed antibiotics and hormones showed signs of slowed development, especially in females. The normal sex ratio observed in M. scalaris from control diets was affected by exposure to caffeine and pharmaceutical mixture treatments. There was an overall effect of treatment on the flies' microbial communities; notably, caffeine fed insects displayed higher microbial variability. Eight bacterial families accounted for approximately 95% of the total microbes in diet and insects. Our results suggest that CECs at environmentally relevant concentrations can affect the biology and microbial communities of an insect of ecological and medical importance.

Polygenic Control of Carotid Atherosclerosis in a BALB/cJ × SM/J Intercross and a Combined Cross Involving Multiple Mouse Strains.

Atherosclerosis in the carotid arteries is a major cause of ischemic stroke, which accounts for 85% of all stroke cases. Genetic factors contributing to carotid atherosclerosis remain poorly understood. The aim of this study was to identify chromosomal regions harboring genes contributing to carotid atherosclerosis in mice. From an intercross between BALB/cJ (BALB) and SM/J (SM) apolipoprotein E-deficient (Apoe-/-) mice, 228 female F2 mice were generated and fed a "Western" diet for 12 wk. Atherosclerotic lesion sizes in the left carotid artery were quantified. Across the entire genome, 149 genetic markers were genotyped. Quantitative trait locus (QTL) analysis revealed eight loci for carotid lesion sizes, located on chromosomes 1, 5, 12, 13, 15, 16, and 18. Combined cross-linkage analysis using data from this cross, and two previous F2 crosses derived from BALB, C57BL/6J and C3H/HeJ strains, identified five significant QTL on chromosomes 5, 9, 12, and 13, and nine suggestive QTL for carotid atherosclerosis. Of them, the QTL on chromosome 12 had a high LOD score of 9.95. Bioinformatic analysis prioritized Arhgap5, Akap6, Mipol1, Clec14a, Fancm, Nin, Dact1, Rtn1, and Slc38a6 as probable candidate genes for this QTL. Atherosclerotic lesion sizes were significantly correlated with non-HDL cholesterol levels (r = 0.254; p = 0.00016) but inversely correlated with HDL cholesterol levels (r = -0.134; p = 0.049) in the current cross. Thus, we demonstrated the polygenic control of carotid atherosclerosis in mice. The correlations of carotid lesion sizes with non-HDL and HDL suggest that genetic factors exert effects on carotid atherosclerosis partially through modulation of lipoprotein homeostasis.

Data on genetic analysis of atherosclerosis identifies a major susceptibility locus in the major histocompatibility complex of mice.

The data presented here are related to the research article, entitled Genetic analysis of atherosclerosis identifies a major susceptibility locus in the major histocompatibility complex of mice, published in Atherosclerosis 2016;254:124 (A.T. Grainger, M.B. Jones, J. Li, M.H. Chen, A. Manichaikul, W. Shi, 2016) [1]. The supporting materials include original genotypic and phenotypic data obtained from 206 female F2 mice derived from an intercross between BALB and SMJ inbred mice. The F2 mice were fed 12 weeks of Western diet, starting at 6 weeks of age. Atherosclerotic lesion size in the aortic root of each mouse is the sum of the top 8 lesion areas. The data is provided in the format required for determining QTLs using two independent programs, J/QTL and PLINK.

Genetic analysis of atherosclerosis identifies a major susceptibility locus in the major histocompatibility complex of mice.

BACKGROUND AND AIMS: Recent genome-wide association studies (GWAS) have identified over 50 significant loci containing common variants associated with coronary artery disease. However, these variants explain only 26% of the genetic heritability of the disease, suggesting that many more variants remain to be discovered. Here, we examined the genetic basis underlying the marked difference between SM/J-Apoe-/- and BALB/cJ-Apoe-/- mice in atherosclerotic lesion formation. METHODS: 206 female F2 mice generated from an intercross between the two Apoe-/- strains were fed 12 weeks of western diet. Atherosclerotic lesion sizes in the aortic root were measured and 149 genetic markers genotyped across the entire genome. RESULTS: A significant locus, named Ath49 (LOD score: 4.18), for atherosclerosis was mapped to the H2 complex [mouse major histocompatibility complex (MHC)] on chromosome 17. Bioinformatic analysis identified 12 probable candidate genes, including Tnfrsf21, Adgrf1, Adgrf5, Mep1a, and Pla2g7. Corresponding human genomic regions of Ath49 showed significant association with coronary heart disease. Five suggestive loci on chromosomes 1, 4, 5, and 8 for atherosclerosis were also identified. Atherosclerotic lesion sizes were significantly correlated with HDL but not with non-HDL cholesterol, triglyceride or glucose levels in the F2 cohort. CONCLUSIONS: We have identified the MHC as a major genetic determinant of atherosclerosis, highlighting the importance of inflammation in atherogenesis.

High-Throughput Genetic Testing for Thrombotic Microangiopathies and C3 Glomerulopathies.

The thrombotic microangiopathies (TMAs) and C3 glomerulopathies (C3Gs) include a spectrum of rare diseases such as atypical hemolytic uremic syndrome, thrombotic thrombocytopenic purpura, C3GN, and dense deposit disease, which share phenotypic similarities and underlying genetic commonalities. Variants in several genes contribute to the pathogenesis of these diseases, and identification of these variants may inform the diagnosis and treatment of affected patients. We have developed and validated a comprehensive genetic panel that screens all exons of all genes implicated in TMA and C3G. The closely integrated pipeline implemented includes targeted genomic enrichment, massively parallel sequencing, bioinformatic analysis, and a multidisciplinary conference to analyze identified variants in the context of each patient's specific phenotype. Herein, we present our 1-year experience with this panel, during which time we studied 193 patients. We identified 17 novel and 74 rare variants, which we classified as pathogenic (11), likely pathogenic (12), and of uncertain significance (68). Compared with controls, patients with C3G had a higher frequency of rare and novel variants in C3 convertase (C3 and CFB) and complement regulator (CFH, CFI, CFHR5, and CD46) genes (P<0.05). In contrast, patients with TMA had an increase in rare and novel variants only in complement regulator genes (P<0.01), a distinction consistent with differing sites of complement dysregulation in these two diseases. In summary, we were able to provide a positive genetic diagnosis in 43% and 41% of patients carrying the clinical diagnosis of C3G and TMA, respectively.

"No level up!": no effects of video game specialization and expertise on cognitive performance.

Previous research into the effects of action video gaming on cognition has suggested that long term exposure to this type of game might lead to an enhancement of cognitive skills that transfer to non-gaming cognitive tasks. However, these results have been controversial. The aim of the current study was to test the presence of positive cognitive transfer from action video games to two cognitive tasks. More specifically, this study investigated the effects that participants' expertise and genre specialization have on cognitive improvements in one task unrelated to video gaming (a flanker task) and one related task (change detection task with both control and genre-specific images). This study was unique in three ways. Firstly, it analyzed a continuum of expertise levels, which has yet to be investigated in research into the cognitive benefits of video gaming. Secondly, it explored genre-specific skill developments on these tasks by comparing Action and Strategy video game players (VGPs). Thirdly, it used a very tight experiment design, including the experimenter being blind to expertise level and genre specialization of the participant. Ninety-two university students aged between 18 and 30 (M = 21.25) were recruited through opportunistic sampling and were grouped by video game specialization and expertise level. While the results of the flanker task were consistent with previous research (i.e., effect of congruence), there was no effect of expertise, and the action gamers failed to outperform the strategy gamers. Additionally, contrary to expectation, there was no interaction between genre specialization and image type in the change detection task, again demonstrating no expertise effect. The lack of effects for game specialization and expertise goes against previous research on the positive effects of action video gaming on other cognitive tasks.

Convergence of potential net ecosystem production among contrasting C3 grasslands.

Metabolic theory and body size constraints on biomass production and decomposition suggest that differences in the intrinsic potential net ecosystem production (NEPPOT ) should be small among contrasting C3 grasslands and therefore unable to explain the wide range in the annual apparent net ecosystem production (NEPAPP ) reported by previous studies. We estimated NEPPOT for nine C3 grasslands under contrasting climate and management regimes using multiyear eddy covariance data. NEPPOT converged within a narrow range, suggesting little difference in the net carbon dioxide uptake capacity among C3 grasslands. Our results indicate a unique feature of C3 grasslands compared with other terrestrial ecosystems and suggest a state of stability in NEPPOT due to tightly coupled production and respiration processes. Consequently, the annual NEPAPP of C3 grasslands is primarily a function of seasonal and short-term environmental and management constraints, and therefore especially susceptible to changes in future climate patterns and associated adaptation of management practices.

A quantitative integrated assessment of pollution prevention achieved by integrated pollution prevention control licensing.

This paper presents an innovative, quantitative assessment of pollution avoidance attributable to environmental regulation enforced through integrated licensing, using Ireland's pharmaceutical-manufacturing sector as a case study. Emissions data reported by pharmaceutical installations were aggregated into a pollution trend using an Environmental Emissions Index (EEI) based on Lifecycle Assessment methodologies. Complete sectoral emissions data from 2001 to 2007 were extrapolated back to 1995, based on available data. Production volume data were used to derive a sectoral production index, and determine 'no-improvement' emission trends, whilst questionnaire responses from 20 industry representatives were used to quantify the contribution of integrated licensing to emission avoidance relative to these trends. Between 2001 and 2007, there was a 40% absolute reduction in direct pollution from 27 core installations, and 45% pollution avoidance relative to hypothetical 'no-improvement' pollution. It was estimated that environmental regulation avoided 20% of 'no-improvement' pollution, in addition to 25% avoidance under business-as-usual. For specific emissions, avoidance ranged from 14% and 30 kt a(-1) for CO(2) to 88% and 598 t a(-1) for SO(x). Between 1995 and 2007, there was a 59% absolute reduction in direct pollution, and 76% pollution avoidance. Pollution avoidance was dominated by reductions in emissions of VOCs, SO(x) and NO(x) to air, and emissions of heavy metals to water. Pollution avoidance of 35% was attributed to integrated licensing, ranging from between 8% and 2.9 t a(-1) for phosphorus emissions to water to 49% and 3143 t a(-1) for SO(x) emissions to air. Environmental regulation enforced through integrated licensing has been the major driver of substantial pollution avoidance achieved by Ireland's pharmaceutical sector - through emission limit values associated with Best Available Techniques, emissions monitoring and reporting requirements, and performance targets specified in environmental management plans. This compliant sector offers a positive, but not necessarily typical, case study of IPPC effectiveness.