First genome-wide association study investigating blood pressure and renal traits in domestic cats.

Hypertension (HTN) and chronic kidney disease (CKD) are common in ageing cats. In humans, blood pressure (BP) and renal function are complex heritable traits. We performed the first feline genome-wide association study (GWAS) of quantitative traits systolic BP and creatinine and binary outcomes HTN and CKD, testing 1022 domestic cats with a discovery, replication and meta-analysis design. No variants reached experimental significance level in the discovery stage for any phenotype. Follow up of the top 9 variants for creatinine and 5 for systolic BP, one SNP reached experimental-wide significance for association with creatinine in the combined meta-analysis (chrD1.10258177; P = 1.34 × 10-6). Exploratory genetic risk score (GRS) analyses were performed. Within the discovery sample, GRS of top SNPs from the BP and creatinine GWAS show strong association with HTN and CKD but did not validate in independent replication samples. A GRS including SNPs corresponding to human CKD genes was not significant in an independent subset of cats. Gene-set enrichment and pathway-based analysis (GSEA) was performed for both quantitative phenotypes, with 30 enriched pathways with creatinine. Our results support the utility of GWASs and GSEA for genetic discovery of complex traits in cats, with the caveat of our findings requiring validation.

Uromodulin gene variants and their association with renal function and blood pressure in cats: a pilot study.

OBJECTIVES: In humans, genome-wide association studies have identified variants in the uromodulin gene (UMOD) associated with blood pressure and renal function. This study aimed to evaluate the association of single nucleotide polymorphisms at the UMOD locus with renal function and blood pressure in cats. METHODS: We retrospectively identified cats aged 14 years that had participated in a geriatric monitoring program, and from which stored DNA samples were available, from a computerised database. We then measured the association of specific single nucleotide polymorphisms in the feline UMOD gene with renal function and systolic blood pressure as continuous variables and, also, the dichotomous outcome of azotaemic chronic kidney disease and systemic hypertension. RESULTS: Eight intronic single nucleotide polymorphisms, one 1372 base pairs upstream from UMOD and two exonic single nucleotide polymorphisms were evaluated in 227 cats with renal and blood pressure data. An analysis of 188 cats found four single nucleotide polymorphisms to be significantly associated (P<0·01) with systolic blood pressure although all were in linkage disequilibrium. No significant associations were identified between single nucleotide polymorphisms and renal function or chronic kidney disease. CLINICAL SIGNIFICANCE: Results of this pilot study suggest that genetic variation in UMOD might influence blood pressure in cats, similar to findings in humans. Validation of these results is required.

Lowering N2O emissions from soils using eucalypt biochar: the importance of redox reactions.

Agricultural soils are the primary anthropogenic source of atmospheric nitrous oxide (N2O), contributing to global warming and depletion of stratospheric ozone. Biochar addition has shown potential to lower soil N2O emission, with the mechanisms remaining unclear. We incubated eucalypt biochar (550 °C)--0, 1 and 5% (w/w) in Ferralsol at 3 water regimes (12, 39 and 54% WFPS)--in a soil column, following gamma irradiation. After N2O was injected at the base of the soil column, in the 0% biochar control 100% of expected injected N2O was released into headspace, declining to 67% in the 5% amendment. In a 100% biochar column at 6% WFPS, only 16% of the expected N2O was observed. X-ray photoelectron spectroscopy identified changes in surface functional groups suggesting interactions between N2O and the biochar surfaces. We have shown increases in -O-C = N /pyridine pyrrole/NH3, suggesting reactions between N2O and the carbon (C) matrix upon exposure to N2O. With increasing rates of biochar application, higher pH adjusted redox potentials were observed at the lower water contents. Evidence suggests that biochar has taken part in redox reactions reducing N2O to dinitrogen (N2), in addition to adsorption of N2O.

Differences between disease-associated endoplasmic reticulum aminopeptidase 1 (ERAP1) isoforms in cellular expression, interactions with tumour necrosis factor receptor 1 (TNF-R1) and regulation by cytokines.

Endoplasmic reticulum aminopeptidase 1 (ERAP1) processes peptides for major histocompatibility complex (MHC) class I presentation and promotes cytokine receptor ectodomain shedding. These known functions of ERAP1 may explain its genetic association with several autoimmune inflammatory diseases. In this study, we identified four novel alternatively spliced variants of ERAP1 mRNA, designated as ΔExon-11, ΔExon-13, ΔExon-14 and ΔExon-15. We also observed a rapid and differential modulation of ERAP1 mRNA levels and spliced variants in different cell types pretreated with lipopolysaccharide (LPS). We have studied three full-length allelic forms of ERAP1 (R127-K528, P127-K528, P127-R528) and one spliced variant (ΔExon-11) and assessed their interactions with tumour necrosis factor receptor 1 (TNF-R1) in transfected cells. We observed variation in cellular expression of different ERAP1 isoforms, with R127-K528 being expressed at a much lower level. Furthermore, the cellular expression of full-length P127-K528 and ΔExon-11 spliced variant was enhanced significantly when co-transfected with TNF-R1. Isoforms P127-K528, P127-R528 and ΔExon-11 spliced variant associated with TNF-R1, and this interaction occurred in a region within the first 10 exons of ERAP1. Supernatant-derived vesicles from transfected cells contained the full-length and ectodomain form of soluble TNF-R1, as well as carrying the full-length ERAP1 isoforms. We observed marginal differences between TNF-R1 ectodomain levels when co-expressed with individual ERAP1 isoforms, and treatment of transfected cells with tumour necrosis factor (TNF), interleukin (IL)-1ß and IL-10 exerted variable effects on TNF-R1 ectodomain cleavage. Our data suggest that ERAP1 isoforms may exhibit differential biological properties and inflammatory mediators could play critical roles in modulating ERAP1 expression, leading to altered functional activities of this enzyme.

Chemical and structural analysis of enhanced biochars: thermally treated mixtures of biochar, chicken litter, clay and minerals.

In this study biochar mixtures comprising a Jarrah-based biochar, chicken litter (CL), clay and other minerals were thermally treated, via torrefaction, at moderate temperatures (180 and 220 °C). The objectives of this treatment were to reduce N losses from CL during processing and to determine the effect of both the type of added clay and the torrefaction temperature on the structural and chemical properties of the final product, termed as an enhanced biochar (EB). Detailed characterisation indicated that the EBs contained high concentrations of plant available nutrients. Both the nutrient content and plant availability were affected by torrefaction temperature. The higher temperature (220 °C) promoted the greater decomposition of organic matter in the CL and dissociated labile carbon from the Jarrah-based biochar, which produced a higher concentration of dissolved organic carbon (DOC). This DOC may assist to solubilise mineral P, and may also react with both clay and minerals to block active sites for P adsorption. This subsequently resulted in higher concentrations of plant available P. Nitrogen loss was minimised, with up to 73% of the initial total N contained in the feedstock remaining in the final EB. However, N availability was affected by both torrefaction temperature and the nature of the clay minerals added.

High quality genomic DNA extraction from postmortem fetal tissue.

OBJECTIVE: We examined the yield and quality of genomic deoxyribonucleic acid (DNA) extracted from various postmortem fetal tissues. METHODS: Fetal tissues were collected at the time of autopsy, and DNA was subsequently extracted. The yield and DNA quality was assessed using ultraviolet spectrometry and agarose gel electrophoresis. We used polymerase chain reaction (PCR) to assess the DNA extracted for genomic testing. RESULTS: The median (range) gestation of the fetuses was 22 (16-41) weeks and the postmortem interval was 5.5 (2-10) days. Non-degraded genomic DNA was successfully extracted from all fetal tissues. Liver tissue had the lowest quality and muscle the highest quality. DNA yield or purity was not influenced by the postmortem interval. CONCLUSION: High quality genomic DNA can be extracted from fetal muscle, despite postmortem intervals of several days.

Analytical electron microscopy of black carbon and microaggregated mineral matter in Amazonian dark Earth.

Black carbon (BC) is one of the most stable forms of soil organic matter. Its surface functional groups and structure have been well characterized by a range of analytical methods. However, little is known about the mechanisms of interactions between the BC particles and the surrounding mineral matter. In this paper a range of microscopy techniques, such as transmission electron microscopy and scanning transmission electron microscopy, were used to investigate the possible reactions of BC particles within microaggregates (<2 mm) found in Amazonian dark Earth. Attention is given to the interactions that occur at the interfacial regions between the organic and inorganic phases. Examination of Amazonian dark Earth showed that the carbon-rich phase detected within the BC particles has a significant calcium concentration and a high density of micropores was found at the BC-mineral interface. These observations provide evidence to support suggested mechanisms of interaction between these phases.

Effect of microstructure upon elastic behaviour of human tooth enamel.

Tooth enamel is the stiffest tissue in the human body with a well-organized microstructure. Developmental diseases, such as enamel hypomineralisation, have been reported to cause marked reduction in the elastic modulus of enamel and consequently impair dental function. We produce evidence, using site-specific transmission electron microscopy (TEM), of difference in microstructure between sound and hypomineralised enamel. Built upon that, we develop a mechanical model to explore the relationship of the elastic modulus of the mineral-protein composite structure of enamel with the thickness of protein layers and the direction of mechanical loading. We conclude that when subject to complex mechanical loading conditions, sound enamel exhibits consistently high stiffness, which is essential for dental function. A marked decrease in stiffness of hypomineralised enamel is caused primarily by an increase in the thickness of protein layers between apatite crystals and to a lesser extent by an increase in the effective crystal orientation angle.

Thickness-dependent phase transformation in nanoindented germanium thin films.

We investigate the mechanical response of 50-600 nm epitaxial Ge films on a Si substrate using nanoindentation with a nominally spherical (R≈4.3 µm) diamond tip. The inelastic deformation mechanism is found to depend critically on the film thickness. Sub-100 nm Ge films deform by pressure-induced phase transformation, whereas thicker films deform only by shear-induced dislocation slip and twinning. Nanoindentation fracture response is similarly dependent on film thickness. Elastic stress modelling shows that differing stress modes vary in their spatial distribution, and consequently the film thickness governs the stress state in the film, in conjunction with the radius of the nanoindenter tip. This opens the prospect of tailoring the contact response of Ge and related materials in thin film form by varying film thickness and indenter radius.

Phenotypic consequences of variation across the aldosterone synthase and 11-beta hydroxylase locus in a hypertensive cohort: data from the MRC BRIGHT Study.

BACKGROUND: Aldosterone is an important cardiovascular hormone; 15% of hypertensive subjects have alteration in aldosterone regulation, defined by a raised ratio of aldosterone to renin (ARR). Studies of the aldosterone synthase gene (CYP11B2) have focused on a single nucleotide polymorphism in the 5'promoter region (-344 C/T). In normotensive subjects, the T allele associates with raised levels of the 11-deoxysteroids, deoxycorticosterone and 11-deoxycortisol which are substrates for 11beta-hydroxylase, encoded by the adjacent and homologous gene, CYP11B1. We have speculated that this altered 11beta-hydroxylase efficiency leads to increased ACTH drive to the adrenal gland to maintain cortisol production and reported herein the association between the -344 C/T single nucleotide polymorphism (SNP) and adrenal steroid production in subjects with essential hypertension. METHODS: The CYP11B2-344 C/T polymorphism was genotyped and urinary excretion of adrenal steroid metabolites was measured (by GCMS) in 511 unrelated hypertensives from the Medical Research Council (MRC) British Genetics of Hypertension (BRIGHT) study. RESULTS: Thirty-five per cent of subjects were homozygous for the -344T allele whilst 16% were CC homozygotes. There was no difference in cortisol excretion rate between the two genotype groups but the index of adrenal 11beta-hydroxylation (ratio of tetrahydrodeoxycortisol/total cortisol) was significantly higher in the TT group (P < 0.005) than in the CC group. Excretion rates of the major urinary metabolite of aldosterone (tetrahydroaldosterone) correlated strongly with the ACTH-regulated steroids, cortisol (r = 0.437, P < 0.0001) and total androgen metabolites (r = 0.4, P < 0.0001) in TT but not CC subjects. CONCLUSIONS: Hypertensives homozygous for the -344 T allele of CYP11B2 demonstrate altered 11beta-hydroxylase efficiency (CYP11B1); this is consistent with the hypothesis of a genetically determined increase in adrenal ACTH drive in these subjects. The correlation between excretion of aldosterone and cortisol metabolites and suggests that, in TT subjects, ACTH exerts an important common regulatory influence on adrenal corticosteroid production in subjects with hypertension.

Imaging and analysis of 3-D structure using a dual beam FIB.

The application of focused ion beam instrumentation in the generation of three-dimensional microstructural data is described. The methodologies used to acquire and manipulate this data are explained, and the technique is illustrated by a number of examples from the material sciences. The limitations of this method, and practical pointers to the generation of meaningful data, are also discussed.

Damage in III-V compounds during focused ion beam milling.

The damage layers generated in III-V compounds exposed to energetic gallium ions in a focused ion beam (FIB) instrument have been characterized by transmission electron microscopy (TEM). The damage on the side walls of the milled trenches is in the form of amorphous layers associated with direct amorphization from the gallium beam, rather than from redeposition of milled material. However, the damage on the bottom of the milled trenches is more complex. For InP and InAs the damage layers include the presence of crystalline phases resulting from recrystallization associated heating from the incident beam and gallium implantation. In contrast, such crystalline phases are not present in GaAs. The thicknesses of the damage layers are greater than those calculated from theoretical models of ion implantation. These differences arise because the dynamic nature of FIB milling means that the energetic ion beams pass through already damaged layers. In InP recoil phosphorus atoms also cause significant damage.

The application of FIB milling for specimen preparation from crystalline germanium.

The effectiveness of focused ion beam (FIB) for preparation of crystalline germanium specimens has been studied. FIB milling results in strong cellular relief of the germanium surfaces on bulk specimens. This cellular relief, associated with the generation of high densities of point defects during interaction of the specimen with the high-energy gallium beam, can be reduced by using either a lower ion beam currents or a lower beam energy. Even under these milling conditions the cellular relief is, however, still evident on the surface of the TEM specimens as evidenced by so-called 'curtaining' relief. Nevertheless good quality specimens for both conventional and high-resolution imaging may be prepared using FIB milling if low currents are employed for final milling.

FIB-induced damage in silicon.

The damage created in silicon transmission electron microscope specimens prepared using a focused ion beam miller is assessed using cross-sections of trenches milled under different beam conditions. Side-wall damage consists of an amorphous layer formed by direct interaction with the energetic gallium ion beam; a small amount of implanted gallium is also detected. By contrast, bottom-wall damage layers are more complex and contain both amorphous films and crystalline regions that are richer in implanted gallium. More complex milling sequences show that redeposition of milled material, enriched in gallium, can occur depending on the geometry of the mill employed. The thickness of the damage layers depends strongly on beam energy, but is independent of beam current. Monte Carlo modelling of the damage formed indicates that recoil silicon atoms contribute significantly to the damaged formed in the specimen.

Genes and hypertension.

The combination of investigation of rare Mendelian forms of hypertension, candidate gene studies, comparative mapping and genome-wide screening in both animal models and man has led to significant progress in determining new mechanisms of blood pressure control. In this review, the newly discovered blood pressure/cardiovascular genes, WNK kinases and angiotensin converting enzyme 2 and the development of a new anti-hypertensive agent PST2238 are discussed. Major genes causing essential hypertension have yet to be discovered, however, there are now over 20 published genome-wide screens for blood pressure controlling genes. Several regions demonstrate suggestive linkage to the trait and there is some overlap of regions between the different studies. It is hoped that new blood pressure genes will ultimately be discovered using this method. Pharmacogenetic studies in hypertension have only been initiated recently, some are described in this paper. Small studies upon single candidate genes, suggest that the contribution of genetics to the inter-individual variation in blood pressure response to anti-hypertensive therapy, is small, approximately 3-5%. Recently micro-arrays with multiple polymorphisms in multiple genes have been used. After accounting for the additive affects of multiple blood pressure loci, an individual's genetic profile appeared to explain up to 50% of the variation in blood pressure response to therapy. Knowledge of the genetic variants that cause hypertension and influence response to anti-hypertensive therapy will ultimately provide a greater understanding of the molecular mechanisms underlying blood pressure control.

Redeposition effects in transmission electron microscope specimens of FeAl-WC composites prepared using a focused ion beam.

Artifacts associated with transmission electron microscope (TEM) specimens prepared using a focused ion beam (FIB) are not well understood, especially those in non-semiconductor materials. In this paper the extent and origins of artifacts associated with redeposition of milled material in TEM specimens of a FeAl--WC metal matrix composite prepared by FIB were investigated. Cross-sections were prepared normal to an initial FIB cut that allowed direct observation of any damage layers, which are believed to be associated with both redeposition of sputtered material and amorphisation of the surface of the specimen by the ion beam. Techniques for the minimisation of redeposition using either final cleaning mills at low accelerating voltages or plasma cleaning were also investigated and found to be ineffective in removing or reducing these damaged layers. TEM cross-sections of specimens treated using low energy mills and plasma cleaning, further confirmed that these techniques did little to reduce any redeposited or amorphous material.

Human chromosome 17 in essential hypertension.

Hypertension affects up to 30% of the adult population in Western societies and is a major risk factor for kidney disease, stroke and coronary heart disease. It is a complex trait thought to be influenced by a number of genes and environmental factors, although the precise aetiology remains unknown at this time. A number of methods have been successfully used to identify mutations that cause Mendelian traits and these are now being applied to the investigation of complex diseases. This review summarises the data gathered, using such approaches, that suggest there is a gene or genes on chromosome 17 causing human essential hypertension. Studies in rodent models are discussed first, followed by studies of human hypertension that include the investigation of pseudohypoaldosteronism type II, a monogenic trait that manifests with hypertension alongside other phenotypic variables. In addition, candidate gene studies, genome screens and linkage studies based on comparative mapping are outlined. To date no gene has been identified on human chromosome 17 that influences blood pressure and causes human essential hypertension. However, results of ongoing fine mapping and candidate gene studies in both rodents and man are eagerly awaited.

Identification of a transactivation motif in the CLN3 protein.

A transactivation motif has been identified in the neurodegenerative disease protein, CLN3. The C-terminal domain (residues 394-438) of CLN3 can function as a transcriptional activator when fused to the DNA binding domain, LexA. A series of deletion and substitution constructs have been generated to identify the essential region for transactivation. A similar motif is also present in the POU domain transcription factor, nubbin. However, this domain alone does not activate transcription, allowing further localisation of the critical residues in CLN3 required for activity.

Analysis of CLN3-protein interactions using the yeast two-hybrid system.

Juvenile neuronal ceroid lipofuscinosis (Batten disease) is a childhood neurodegenerative disease that is caused by mutations in the CLN3 gene. The protein encoded by CLN3 has no homology with any proteins of known function and its cellular role remains elusive. In order to investigate the role played by the CLN3 protein we aimed to identify interacting proteins. Here, we describe the yeast two-hybrid system as the approach taken to investigate such protein-protein interactions. CLN3 was expressed as a fusion protein with a DNA-binding domain and used to screen a library of human fetal brain cDNAs fused to a transcriptional activation domain. Owing to low level expression of the full length CLN3 fusion protein, truncated regions corresponding to the predicted hydrophilic regions were also tested. No proteins that interact with CLN3 were detected, nor was there any evidence for CLN3-CLN3 interactions. Potential interaction of CLN3 with subunit c of mitochondrial ATP synthase, the major component of the storage material that accumulates in Batten disease patients, was also tested. No interaction was detected suggesting that the accumulation of subunit c does not result from loss of a process that requires a direct interaction with CLN3. We conclude that either CLN3 does not interact with other proteins or such interactions cannot be detected using the two-hybrid system.

Pseudoexon activation as a novel mechanism for disease resulting in atypical growth-hormone insensitivity.

Inherited growth-hormone insensitivity (GHI) is a heterogeneous disorder that is often caused by mutations in the coding exons or flanking intronic sequences of the growth-hormone receptor gene (GHR). Here we describe a novel point mutation, in four children with GHI, that leads to activation of an intronic pseudoexon resulting in inclusion of an additional 108 nt between exons 6 and 7 in the majority of GHR transcripts. This mutation lies within the pseudoexon (A(-1)-->G(-1) at the 5' pseudoexon splice site) and, under in vitro splicing conditions, results in inclusion of the mutant pseudoexon, whereas the wild-type pseudoexon is skipped. The presence of the pseudoexon results in inclusion of an additional 36-amino acid sequence in a region of the receptor known to be involved in homo-dimerization, which is essential for signal transduction.