The Association Between Ascorbate and the Hypoxia-Inducible Factors in Human Renal Cell Carcinoma Requires a Functional Von Hippel-Lindau Protein

Hypoxia-inducible transcription factors (HIFs) drive angiogenesis and cancer cell growth, contributing to an aggressive tumor phenotype. HIF-α protein levels and activity are controlled at the post-translational level by HIF hydroxylases. Hydroxylated HIF-α is recognized by the von Hippel Lindau (VHL) tumor suppressor and targeted for degradation. The HIF hydroxylases are members of the iron and 2-oxoglutarate-dependent dioxygenases, which require ascorbate as cofactor for activity. Clear cell renal cell carcinomas (ccRCC) harbor mutations in the VHL gene, whereas papillary RCC (pRCC) have a functional VHL. These natural occurring VHL variants in RCC enable the testing, in clinical samples, of the hypothesis that ascorbate modulates HIF-α levels through its role as a cofactor for the HIF hydroxylases. We measured ascorbate, HIF-1α, and HIF-2α protein and HIF downstream targets BNIP3, CA9, cyclin D1, GLUT1, and VEGF (combined to generate the HIF pathway score) in VHL-defective ccRCC (n = 73) and VHL-proficient pRCC human tumor tissue (n = 41). HIF and ascorbate levels were increased in ccRCC and pRCC tumors compared to matched renal cortex. HIF-1 and total HIF pathway activation scores were decreased with higher ascorbate in pRCC tumors (Spearman r = −0.38, p < 0.05 and r = −0.35, p < 0.05). This was not evident for ccRCC tumors. In mechanistic studies in vitro, ascorbate influenced HIF-1 activity in VHL-proficient, but not VHL-defective ccRCC cells. Our results indicate that ccRCC, which lacks a functional VHL, does not respond to ascorbate-mediated modulation of the HIF response. This contrasts with the demonstrated association between ascorbate content and the HIF pathway observed in pRCC and other tumors with a functional VHL. The results support a role for ascorbate as a modulator of HIF activity and tumor aggression in cancer types with a functional hypoxic response

Tumour growth in mice resistant to diet-induced obesity

Obesity is a chronic disease with associated increases in the incidence, and a reduction in survival, of many cancer types. Obesity results from an imbalance in calorie intake and calorie requirement. This study aimed to investigate the separate effects of high-fat diet and obesity on cancer in an animal model resistant to diet-induced obesity. Male BALB/c mice fed long-term on a high-fat, Western-style diet were implanted with syngeneic CT26 colon adenocarcinoma cells and compared to mice fed normal diet. BALB/c mice on high-fat diet were 10% heavier than mice fed normal diet, with no difference in tumour growth rates or tumour cell proliferation. Subgroups of mice that became obese on high-fat diet, however, showed increased tumour growth rates compared to mice fed normal diet, whereas mice that remained slim showed no difference in tumour growth. Protein arrays identified several adipokines that were expressed at different levels, including serum Tissue Inhibitors of Metallo-Proteinases (TIMP-1) and tumour C-Reactive Protein (CRP). In conclusion, tumour growth was enhanced in mice unable to resist obesity, and adipokine profiles were affected by the animals’ ability to resist obesity

Analysis of Fcγ receptor haplotypes in rheumatoid arthritis: FCGR3A remains a major susceptibility gene at this locus, with an additional contribution from FCGR3B

The Fcγ receptors play important roles in the initiation and regulation of many immunological and inflammatory processes, and genetic variants (FCGR) have been associated with numerous autoimmune and infectious diseases. The data in rheumatoid arthritis (RA) are conflicting and we previously demonstrated an association between FCGR3A and RA. In view of the close molecular proximity with FCGR2A, FCGR2B and FCGR3B, additional polymorphisms within these genes and FCGR haplotypes were examined to refine the extent of association with RA. Biallelic polymorphisms in FCGR2A, FCGR2B and FCGR3B were examined for association with RA in two well characterized UK Caucasian and North Indian/Pakistani cohorts, in which FCGR3A genotyping had previously been undertaken. Haplotype frequencies and linkage disequilibrium were estimated across the FCGR locus and a model-free analysis was performed to determine association with RA. This was followed by regression analysis, allowing for phase uncertainty, to identify the particular haplotype(s) that influences disease risk. Our results reveal that FCGR2A, FCGR2B and FCGR3B were not associated with RA. The haplotype with the strongest association with RA susceptibility was the FCGR3A–FCGR3B 158V-NA2 haplotype (odds ratio 3.18, 95% confidence interval 1.13–8.92 [P = 0.03] for homozygotes compared with all genotypes). The association was stronger in the presence of nodules (odds ratio 5.03, 95% confidence interval 1.44–17.56; P = 0.01). This haplotype was also more common in North Indian/Pakistani RA patients than in control individuals, but not significantly so. Logistic regression analyses suggested that FCGR3A remained the most significant gene at this locus. The increased association with an FCGR3A–FCGR3B haplotype suggests that other polymorphic variants within FCGR3A or FCGR3B, or in linkage disequilibrium with this haplotype, may additionally contribute to disease pathogenesis

Experimental evidence for drought induced alternative stable states of soil moisture

Ecosystems may exhibit alternative stable states (ASS) in response to environmental change. Modelling and observational data broadly support the theory of ASS, however evidence from manipulation experiments supporting this theory is limited. Here, we provide long-term manipulation and observation data supporting the existence of drought induced alternative stable soil moisture states (irreversible soil wetting) in upland Atlantic heath, dominated by Calluna vulgaris (L.) Hull. Manipulated repeated moderate summer drought, and intense natural summer drought both lowered resilience resulting in shifts in soil moisture dynamics. The repeated moderate summer drought decreased winter soil moisture retention by ~10%. However, intense summer drought, superimposed on the experiment, that began in 2003 and peaked in 2005 caused an unexpected erosion of resilience and a shift to an ASS; both for the experimental drought manipulation and control plots, impairing the soil from rewetting in winter. Measurements outside plots, with vegetation removal, showed no evidence of moisture shifts. Further independent evidence supports our findings from historical soil moisture monitoring at a long-term upland hydrological observatory. The results herald the need for a new paradigm regarding our understanding of soil structure, hydraulics and climate interaction

Fifty years of reduction in sulphur deposition drives recovery in soil pH and plant communities

1. Sulphur deposition through rainfall has led to species loss and ecosystem degradation globally, and across Europe huge reductions in sulphur emissions since the 1970s were expected to promote the recovery of acidified ecosystems. However, the rate and ecological impact of recovery from acidification in terrestrial ecosystems is still unclear as is the influence of management and climate, as to date there has been no long-term spatially extensive evaluation of these changes. 2. Here, we present data from thousands of sites across Great Britain (pH range 3.3–8.7) surveyed repeatedly from 1978–2019 and assess change in soil pH and plant acidity preference (Ellenberg R) in response to atmospheric deposition of sulphur and nitrogen. We analyse change in grasslands managed for pasture, referred to as high-intensity habitats, and compare to seminatural habitats comprising rough grassland, broadleaved woodland, bog and heathland, referred to as low-intensity habitats. 3. Soil pH increased from 1978 to 2007 but then decreased between 2007 and 2019, resulting in a net increase of ~0.2 pH units in low-intensity habitats but no change in high-intensity habitats. The community average Ellenberg R increased in seminatural habitats by ~0.2 units but remained stable in intensive grasslands. 4. In seminatural habitats, but not intensive grasslands, these changes in plant community composition were associated with the soil pH changes which were in turn linked to decreasing sulphur deposition and differences in rainfall. 5. Nitrogen deposition, which was relatively stable over the survey period, showed no additional effect upon soil acidity once sulphur deposition was accounted for. 6. Synthesis: Our results provide conclusive evidence that reductions in acid emissions are stimulating the gradual recovery of chronically acidified terrestrial ecosystems at a whole-country scale, while also suggesting this recovery is being compromised by changing climate and land management

A diversity of diversities: do complex environmental effects underpin associations between below‐ and above‐ground taxa?

•1. To predict how biodiversity will respond to global change, it is crucial to understand the relative roles of abiotic drivers and biotic interactions in driving associations between the biodiversity of disparate taxa. It is particularly challenging to understand diversity–diversity links across domains and habitats, because data are rarely available for multiple above- and below-ground taxa across multiple sites. •2. Here, we analyse data from a unique biodiversity data set gathered across a variety of oceanic temperate terrestrial habitats in Wales, comprising 300 sites with co-located soil microbial, plant, bird and pollinator surveys along with climate and soil physicochemical information. Soil groups are analysed using metabarcoding of the 16S, ITS1 and 18S DNA regions, allowing in-depth characterisation of microbial and soil animal biodiversity. •3. We explore biodiversity relationships along three aspects of community composition: First, we assess correlation between the alpha diversity of different groups. Second, we assess whether biotic turnover between sites is correlated across different groups. Finally, we investigate the co-occurrence of individual taxa across sites. In each analysis, we assess the contribution of linear or nonlinear environmental effects. •4. We find that a positive correlation between alpha diversity of plants, soil bacteria, soil fungi, soil heterotrophic protists, bees and butterflies is in fact driven by complex nonlinear responses to abiotic drivers. In contrast, environmental variation did not account for positive associations between the diversity of plants and both birds and AM fungi, suggesting a role for biotic interactions. •5. Both the diversity and taxon-level associations between the differing soil groups remained even after accounting for nonlinear environmental gradients. Above-ground, spatial factors played larger roles in driving biotic communities, while linear environmental gradients were sufficient to explain many group- and taxon-level relationships. •6. Synthesis. Our results show how nonlinear responses to environmental gradients drive many of the relationships between plant biodiversity and the biodiversity of above- and below-ground biological communities. Our work shows how different aspects of biodiversity might respond nonlinearly to changing environments and identifies cases where management-induced changes in one community could either influence other taxa or lead to loss of apparent biological associations

Soil carbon determination for long‐term monitoring revisited using thermo‐gravimetric analysis

Soils and the vadose zone are the major terrestrial repository of carbon (C) in the form of soil organic matter (SOM), more resistant black carbon (BC), and inorganic carbonate. Differentiating between these pools is important for assessing vulnerability to degradation and changes in the C cycle affecting soil health and climate regulation. Major monitoring programs from field to continent are now being undertaken to track changes in soil carbon (SC). Inexpensive, robust measures that can differentiate small changes in the C pools in a single measurement are highly desirable for long-term monitoring. In this study, we assess the accuracy and precision of thermo-gravimetric analysis (TGA) using organic matter standards, clay minerals, and soils from a national data set. We investigate the use of TGA to routinely differentiate between C pools, something no single measurement has yet achieved. Based on the kinetic nature of thermal oxidation of SC combined with the different thermodynamic stabilities of the molecules, we designed a new method to quantify the inorganic and organic SC and further separate the organic biogeochemically active SOM (as loss on ignition, LOI) from the resistant BC in soils. We analyze the TGA spectrums of a national soil monitoring data set (n = 456) and measure total carbon (TC) using thermal oxidation and also demonstrate a TC/LOI relationship of 0.55 for soils ranging from mineral soils to peat for the United Kingdom consistent with previous monitoring campaigns

Linkage analysis and exome sequencing identify a novel mutation in KCTD7 in patients with progressive myoclonus epilepsy with ataxia

Epilepsy affects approximately 1% of the world\u27s population. Genetic factors and acquired etiologies, as well as a range of environmental triggers, together contribute to epileptogenesis.Wehave identified a family with three daughters affected with progressive myoclonus epilepsy with ataxia. Clinical details of the onset and progression of the neurologic presentation, epileptic seizures, and the natural history of progression over a 10-year period are described. Using autozygosity genetic mapping, we identified a high likelihood homozygous region on chromosome 7p12.1-7q11.22. We subsequently applied whole-exome sequencing and employed a rare variant prioritization analysis within the homozygous region. We identified p.Tyr276Cys in the potassium channel tetramerization domain-containing seven gene, KCTD7, which is expressed predominantly in the brain. Mutations in this gene have been implicated previously in epileptic phenotypes due to disturbances in potassium channel conductance. Pathogenicity of the mutation was supported by bioinformatic predictive analyses and variant cosegregation within the family. Further biologic validation is necessary to fully characterize the pathogenic mechanisms that explain the phenotypic causes of epilepsy with ataxia in these patients

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems

Soil biota accounts for ~25% of global biodiversity and is vital to nutrient cycling and primary production. There is growing momentum to study total belowground biodiversity across large ecological scales to understand how habitat and soil properties shape belowground communities. Microbial and animal components of belowground communities follow divergent responses to soil properties and land use intensification; however, it is unclear whether this extends across heterogeneous ecosystems. Here, a national-scale metabarcoding analysis of 436 locations across 7 different temperate ecosystems shows that belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent trends, whereas β-diversity does not. Animal richness is governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. Our findings demonstrate that established divergent patterns of belowground microbial and animal diversity are consistent across heterogeneous land uses and are detectable using a standardised metabarcoding approach

Beyond taxonomic identification: integration of ecological responses to a soil bacterial 16S rRNA gene database

High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios