Phosphorus desorption and isotope exchange kinetics in agricultural soils

To improve phosphorus (P) fertilization and environmental assessments, a better understanding of release kinetics of solid-phase P to soil solution is needed. In this study, Fe (hydr)oxide-coated filter papers (Fh papers), isotopic exchange kinetics (IEK) and chemical extractions were used to assess the sizes of fast and slowly desorbing P pools in the soils of six long-term Swedish field experiments. The P desorption data from the Fh-paper extraction of soil (20 days of continual P removal) were fitted with the Lookman two-compartment desorption model, which estimates the pools of fast (Q(1)) and slowly (Q(2)) desorbing P, and their desorption rates k(1) and k(2). The amounts of isotope-exchangeable P (E) were calculated (E-1min to E->3 months) and compared with Q(1) and Q(2). The strongest relationship was found between E-1 min and Q(1) (r(2) = .87, p < .01). There was also an inverse relationship between the IEK parameter n (the rate of exchange) and k(1) (r(2) = .52, p < .01) and k(2) (r(2) = .52, p < .01), suggesting that a soil with a high value of n desorbs less P per time unit. The relationships between these results show that they deliver similar information, but both methods are hard to implement in routine analysis. However, Olsen-extractable P was similar in magnitude to Q(1) (P-Olsen = 1.1 x Q(1) + 2.3, r(2) = .96), n and k(1) were related to P-Olsen/P-CaCl2, while k(2) was related to P-oxalate/P-Olsen. Therefore, these extractions can be used to estimate the sizes and desorption rates of the different P pools, which could be important for assessments of plant availability and leaching

Phosphorus dynamics in a tropical forest soil restored after strip mining

Background and aims We hypothesized that successful early ecosystem and soil development in these P-deficient soil materials will initially depend on effective re-establishment of P storage and cycling through organic matter. This hypothesis was tested in a 26-year chronosequence of seven lightly fertilized, oxidic soil materials restored to eucalypt forest communities after bauxite mining. Methods Total P (Pt) status, Hedley P fractions and partial chemical speciation (NaOH-EDTA extraction and analysed using solution 31P NMR spectroscopy) were determined in the restored soils. Results Concentrations of Pt and most Hedley fractions changed with restoration period, declined with depth and were strongly positively correlated with C and N concentrations. Biological P dominated the Labile and Intermediate P fractions while Long-term P was dominantly inorganic. Organic P concentrations in NaOH-EDTA extracts and their chemical natures were similar in restored and unburned native forest sites. Phosphomonoesters were the dominant class of organic P. Conclusions Surprisingly rapid P accretion and fractional changes occurred over 26 years, largely in the surface soils and closely associated with organic matter status. Alkaline hydrolysis products of phosphodiesters and pyrophosphate indicated the importance of microbial P cycling. The important consequences for long-term ecosystem development and biological diversity require further study

Targeted genetic analysis in a large cohort of familial and sporadic cases of aneurysm or dissection of the thoracic aorta

PURPOSE: Thoracic aortic aneurysm/aortic dissection (TAAD) is a disorder with highly variable age of onset and phenotype. We sought to determine the prevalence of pathogenic variants in TAAD-associated genes in a mixed cohort of sporadic and familial TAAD patients and identify relevant genotype–phenotype relationships. METHODS: We used a targeted polymerase chain reaction and next-generation sequencing–based panel for genetic analysis of 15 TAAD-associated genes in 1,025 unrelated TAAD cases. RESULTS: We identified 49 pathogenic or likely pathogenic (P/LP) variants in 47 cases (4.9% of those successfully sequenced). Almost half of the variants were in nonsyndromic cases with no known family history of aortic disease. Twenty-five variants were within FBN1 and two patients were found to harbor two P/LP variants. Presence of a related syndrome, younger age at presentation, family history of aortic disease, and involvement of the ascending aorta increased the risk of carrying a P/LP variant. CONCLUSION: Given the poor prognosis of TAAD that is undiagnosed prior to acute rupture or dissection, genetic analysis of both familial and sporadic cases of TAAD will lead to new diagnoses, more informed management, and possibly reduced mortality through earlier, preclinical diagnosis in genetically determined cases and their family members

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

A genome-wide association study identifies risk alleles in plasminogen and P4HA2 associated with giant cell arteritis

Giant cell arteritis (GCA) is the most common form of vasculitis in individuals older than 50 years in Western countries. To shed light onto the genetic background influencing susceptibility for GCA, we performed a genome-wide association screening in a well-powered study cohort. After imputation, 1,844,133 genetic variants were analysed in 2,134 cases and 9,125 unaffected controls from ten independent populations of European ancestry. Our data confirmed HLA class II as the strongest associated region (independent signals: rs9268905, P = 1.94E-54, per-allele OR = 1.79; and rs9275592, P = 1.14E-40, OR = 2.08). Additionally, PLG and P4HA2 were identified as GCA risk genes at the genome-wide level of significance (rs4252134, P = 1.23E-10, OR = 1.28; and rs128738, P = 4.60E-09, OR = 1.32, respectively). Interestingly, we observed that the association peaks overlapped with different regulatory elements related to cell types and tissues involved in the pathophysiology of GCA. PLG and P4HA2 are involved in vascular remodelling and angiogenesis, suggesting a high relevance of these processes for the pathogenic mechanisms underlying this type of vasculitis

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The structural composition of soil phosphomonoesters as determined by solution 31P NMR spectroscopy and transverse relaxation (T2) experiments

ISSN:0016-7061ISSN:1872-625

Soil phosphomonoesters in large molecular weight material comprise multiple components

The majority of soil organic P is typically that of “unresolved” phosphomonoesters, which are associated with organic P (Po) in large molecular weight (MW) fractions. However, the composition of this pool of Po remains unclear and could contain more than one component. Our aim was to identify the number and nature of components in soil extracts of different MW using solution 31P nuclear magnetic resonance (NMR) spectroscopy and spectral deconvolution fitting. Three surface soils were collected from native sites, which were extracted for Po using 0.25 M NaOH + 0.05 M Na2–EDTA (unfractionated), followed by size separation using ultrafiltration, resulting in four MW fractions (>10 kDa, 3 kDa, and 10-kDa fraction comprised up to 10 components of varying linewidth (0.5–18.6 Hz) and a broad signal (228 Hz). This broad signal was also present in the <3-kDa fraction, albeit at a lower concentration (average was 29% of that in the unfractionated extracts). Furthermore, solution 31P NMR spectra on the <3-kDa fraction revealed a diversity of sharp signals (up to 28) in the phosphomonoester region. Overall, our findings show that soil phosphomonoesters in large MW fractions comprise multiple components of varying linewidth.ISSN:0361-5995ISSN:1435-066