A Genetic Risk Score Distinguishes Different Types of Autoantibody-Mediated Membranous Nephropathy.

Introduction: Membranous nephropathy (MN) is the leading cause of nephrotic syndrome in adults and is characterized by detectable autoantibodies against glomerular antigens, most commonly phospholipase A2 receptor 1 (PLA2R1) and thrombospondin type-1 domain containing 7A (THSD7A). In Europeans, genetic variation in at least five loci, PLA2R1, HLA-DRB1, HLA-DQA1, IRF4, and NFKB1, affects the risk of disease. Here, we investigated the genetic risk differences between different autoantibody states. Methods: 1,409 MN individuals were genotyped genome-wide with a dense SNV array. The genetic risk score (GRS) was calculated utilizing the previously identified European MN loci, and results were compared with 4,929 healthy controls and 422 individuals with steroid-sensitive nephrotic syndrome. Results: GRS was calculated in the 759 MN individuals in whom antibody status was known. The GRS for MN was elevated in the anti-PLA2R1 antibody-positive (N = 372) compared with both the unaffected control (N = 4,929) and anti-THSD7A-positive (N = 31) groups (p < 0.0001 for both comparisons), suggesting that this GRS reflects anti-PLA2R1 MN. Among PLA2R1-positive patients, GRS was inversely correlated with age of disease onset (p = 0.009). Further, the GRS in the dual antibody-negative group (N = 355) was intermediate between controls and the PLA2R1-positive group (p < 0.0001). Conclusion: We demonstrate that the genetic risk factors for PLA2R1- and THSD7A-antibody-associated MN are different. A higher GRS is associated with younger age of onset of disease. Further, a proportion of antibody-negative MN cases have an elevated GRS similar to PLA2R1-positive disease. This suggests that in some individuals with negative serology the disease is driven by autoimmunity against PLA2R1.

Concentric DNA Amplifier That Streamlines In-Solution Biorecognition and On-Particle Biocatalysis.

Colloidal nanoparticle biosensors capable of on-particle biocatalysis are powerful tools for amplified detection of biomolecules. The development and practical uses of such concentric amplifiers can be complicated because of the on-particle biorecognition that involves varying interfacial factors at the biomolecule-nanoparticle interfaces. Herein, we reason that a nanoparticle biosensor equipped with an in-solution biorecognition element may be better fabricated, predicted, controlled, and performed. The in-solution biorecognition shall also be streamlined with the on-particle biocatalysis so that the overall analytical and kinetic performance is not compromised. As a testbed, we introduce a concentric DNA amplifier driven by an enzyme-powered three-dimensional DNA nanomachine, where a DNA walker can be instantly assembled onto a spherical nucleic acid (SNA) track through a polyadenosine anchor. As such, the free DNA walker can participate in reactions in a homogeneous solution before assembling to the SNA track. The instant and stable assembly enabled by both adsorption and complementary base pairing also ensures rapid on-particle biocatalysis. We demonstrate that the in-solution biorecognition effectively eliminates the binding hindrance encountered by the on-particle biorecognition and thus significantly reduced energy barriers for the detection of nucleic acids and proteins. Because of the in-solution biorecognition, our system can also be plugged readily into complex DNA strand displacement networks for rapid signal amplification.

Probing and Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces Using Stochastic DNA Walkers.

Herein, we report a bottom-up approach to assemble a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the bio-nano interface. We systematically investigated the impact of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic behaviors at the interfaces of spherical nucleic acids. Our mechanistic study has revealed critical roles of various interfacial factors that significantly alter molecular binding and enzymatic behaviors from bulk solutions. The improved understanding of the bio-nano interface may facilitate better design and operation of nanoparticle-based biosensors and/or functional devices. We successfully demonstrate how improved understanding of the bio-nano interface help rationalize the design of amplifiable biosensors for nucleic acids and antibodies.

Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants.

Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity. We also introduced an auxiliary probe, a molecular fuel capable of tuning the device in solution via noncovalent catalysis. Collectively, our device produced discrimination factors comparable with commonly used molecular probes but improved the assay sensitivity by ∼100 times. Our results also demonstrate that rationally designed DNA probes through computer simulation can be used to quantitatively improve the design and operation of complexed molecular devices and sensors.

Comparison of soil analytical methods for estimating wheat potassium fertilizer requirements in response to contrasting plant K demand in the glasshouse.

The traditional soil potassium (K) testing methods fail to accurately predict K requirement by plants. The Diffusive Gradients in Thin-films (DGT) method is promising, but the relationship between the DGT-measured K pool and plant available K is not clear. Wheat (Triticum aestivum L., cv. Frame) was grown in 9 Australian broad acre agricultural soils in a glasshouse trial until the end of tillering growth stage (GS30) with different plant K demands generated by varying plant numbers and pot sizes. Different K concentrations in soils were varied by 4 rates of K fertilizer application. The relative dry matter and K uptake were plotted against the soil K test value (CaCl2, Colwell and NH4OAc and DGT K measurements). To obtain 90% of maximum relative dry matter at low root density (closest to field conditions), the critical value of the NH4OAc K method was 91 (R2 = 0.56) mg kg-1. The DGT K method was not able to accurately predict relative dry matter or K uptake due to a weak extraction force for K from soils with high CEC values. Further endeavor on increasing K extraction force of the DGT method is warranted to obtain accurate plant available K results.

Diffusive gradients in thin films measurement of sulfur stable isotope variations in labile soil sulfate.

A diffusive gradient in thin films (DGT) technique, based on a strongly basic anion exchange resin (Amberlite IRA-400), was successfully tested for 34S/32S analysis in labile soil sulfate. Separation of matrix elements (Na, K, and Ca) that potentially cause non-spectral interferences in 34S/32S analysis by MC ICP-MS (multi-collector inductively coupled plasma-mass spectrometry) during sampling of sulfate was demonstrated. No isotopic fractionation caused by diffusion or elution of sulfate was observed below a resin gel disc loading of ≤79 µg S. Above this threshold, fractionation towards 34S was observed. The method was applied to 11 different topsoils and one mineral soil profile (0-100 cm depth) and compared with soil sulfate extraction by water. The S amount and isotopic ratio in DGT-S and water-extractable sulfate correlated significantly (r 2 = 0.89 and r 2 = 0.74 for the 11 topsoils, respectively). The systematically lower 34S/32S isotope ratios of the DGT-S were ascribed to mineralization of organic S.

Novel diffusive gradients in thin films technique to assess labile sulfate in soil.

A novel diffusive gradients in thin films (DGT) technique for sampling labile soil sulfate was developed, based on a strong basic anion exchange resin (Amberlite IRA-400) for sulfate immobilization on the binding gel. For reducing the sulfate background on the resin gels, photopolymerization was applied instead of ammonium persulfate-induced polymerization. Agarose cross-linked polyacrylamide (APA) hydrogels were used as diffusive layer. The sulfate diffusion coefficient in APA gel was determined as 9.83 × 10(-6) ± 0.35 × 10(-6) cm(2) s(-1) at 25 °C. The accumulated sulfate was eluted in 1 mol L(-1) HNO3 with a recovery of 90.9 ± 1.6 %. The developed method was tested against two standard extraction methods for soil sulfate measurement. The obtained low correlation coefficients indicate that DGT and conventional soil test methods assess differential soil sulfate pools, rendering DGT a potentially important tool for measuring labile soil sulfate.

Enzyme-Powered Three-Dimensional DNA Nanomachine for DNA Walking, Payload Release, and Biosensing.

Herein, we report a DNA nanomachine, built from a DNA-functionalized gold nanoparticle (DNA-AuNP), which moves a DNA walker along a three-dimensional (3-D) DNA-AuNP track and executes the task of releasing payloads. The movement of the DNA walker is powered by a nicking endonuclease that cleaves specific DNA substrates on the track. During the movement, each DNA walker cleaves multiple substrates, resulting in the rapid release of payloads (predesigned DNA sequences and their conjugates). The 3-D DNA nanomachine is highly efficient due to the high local effective concentrations of all DNA components that have been co-conjugated on the same AuNP. Moreover, the activity of the 3-D DNA nanomachine can be controlled by introducing a protecting DNA probe that can hybridize to or dehybridize from the DNA walker in a target-specific manner. This property allows us to tailor the DNA nanomachine into a DNA nanosensor that is able to achieve rapid, isothermal, and homogeneous signal amplification for specific nucleic acids in both buffer and a complicated biomatrix.

Application of the diffusive gradients in thin films technique for available potassium measurement in agricultural soils: effects of competing cations on potassium uptake by the resin gel.

The utilization of Amberlite (IRP-69 ion-exchange resin, 100-500 wet mesh) as the binding phase in the diffusive gradients in thin films (DGT) technique has shown potential to improve the assessment of plant-available K in soils. The binding phase has recently been optimized by using a mixed Amberlite and ferrihydrite (MAF) gel which results in linear K uptake over extended deployment periods and in solutions with higher K concentrations. As restriction of K uptake by Ca on the Amberlite based resin gel has been previously proposed, potential competing effects of Ca(2+), Mg(2+) and NH(4+) on K uptake by the MAF gel were investigated. These cations had no effect on K elution efficiency which was 85%. However, K uptake by the MAF gel was restricted in the presence of competing cations in solution. Consequently, the diffusion coefficient of K decreased in the presence of cations compared to previous studies but was stable at 1.12×10(-5)cm(2)s(-1) at 25°C regardless of cation concentrations. Uptake of K by the DGT device was affected by the presence of excessive Ca in more than 30% of twenty typical Australian agricultural soils. However, this problem could be circumvented by using a shorter deployment time than the normal 24 h. Moderate correlation of concentrations of K extracted by DGT with Colwell K (extracted by NaHCO(3), R(2)=0.69) and NH4OAc K (R(2)=0.61) indicates that DGT measures a different pool of K in soils than that measured by the standard extractants used. In addition, the MAF gel has the ability to measure Ca and Mg simultaneously.

Optimization of the diffusive gradients in thin films (DGT) method for simultaneous assay of potassium and plant-available phosphorus in soils.

Potassium (K) and phosphorus (P) are two important macronutrients for crops, and are usually applied to soils as granular fertilizer before seeding. Therefore, accurate soil tests prior to planting to predict crop response to fertilizers are important in optimizing crop yields. Traditional methods used for testing both available K and P in soils, which are based on chemical extraction procedures, are to be soil-type dependent, and the predictive relationships across a broad range of soils are generally poor. The diffusive gradients in thin films (DGT) technique, based on diffusion theory, is extensively used to measure the diffusive supply of trace elements, metals and some nutrients in soils and water. When DGT is used to assess plant-available P in soils, a good relationship is found between crop response to P fertilizer and concentrations of P in soil measured by DGT, and therefore the DGT method provides a more precise recommendation of P fertilizer requirements. Adaptation of the DGT method to measure plant-available K in soils has already been attempted [1], but limitations were reported due to the non-uniform size of the resin gel, decreased K binding rate of the gel at long deployment times and a limited ability to measure a wide range of K concentrations. To eliminate these problems, a new resin gel has been developed by combining Amberlite and ferrihydrite. This mixed Amberlite and ferrihydrite (MAF) gel has improved properties in terms of handling and even distribution of Amberlite in the gel. The elution efficiencies of the MAF gel for K and P were 90% and 96%, respectively. The diffusion coefficient of K through the diffusive gel was 1.30 × 10(-5)cm(2)s(-1) at 22 ± 1°C and was stable through time. Since ferrihydrite is already used in DGT P testing, the ability of the MAF gel to assess available P simultaneously was also assessed. The MAF gel performed the same as the traditional ferrihydrite gel for available P assessment in a wide variety of agricultural soils. This means that the newly developed gel has the potential to measure K and plant-available P in soils simultaneously.

Investigating chemical constraints to the measurement of phosphorus in soils using diffusive gradients in thin films (DGT) and resin methods.

The effect of potential chemical constraints on the performance of two relatively new soil P testing methods, anion exchange membrane (AEM) and diffusive gradients in thin films (DGT), were evaluated. Exposures to ranges of anion (Cl(-), NO(3)(-), SO(4)(2-) and HCO(3)(-)) concentrations relevant to agricultural soils had minimal effect on P recoveries using DGT. It has also been shown previously that DGT P recoveries are unaffected by varying pH (3-9). In contrast, increasing NO(3)(-) and SO(4)(2-) concentrations in solution reduced the recovery of P using the resin method (anion exchange membrane, AEM) by 24% at 50mgL(-1) NO(3)(-) and by 47% at 12mgL(-1) SO(4)(2-) when the P concentration of the test solution was 2mgL(-1). Phosphorus sorption by the resin decreased with increasing Cl(-) concentrations until there was a 100% decrease at 300mgL(-1) Cl(-) when the P concentration of the test solution was 2mgL(-1) and a 92% reduction at 700mgL(-1) Cl(-) when the P concentration of the test solution was 0.2mgL(-1). There was also a small but significant effect of carbonate species on P sorption to the resin at carbonate concentrations that can occur in agricultural soils. Changing the pH of the solution had minimal effects on the resin P measurements in solutions above pH 4, but below pH 4, resin P measurements decreased dramatically. A poor coefficient of determination for the regression fit between DGT and resin measurements on eight agricultural soils suggested that these two methods are measuring different amounts of P for different soils. Resin P measurements increased significantly, but non-uniformly across soils, when the soil:water ratio was decreased but this did not result in an improved relationship with DGT P. There was a minimal effect on measured P using either Cl(-) or HCO(3)(-) as counter ions on the resin.

Performance of a mixed binding layer for measuring anions and cations in a single assay using the diffusive gradients in thin films technique.

The performance of a mixed binding layer (MBL) for use in diffusive gradients in thin films (DGT) was investigated. The MBL consisted of ferrihydrite and Chelex-100 cation-exchange resin combined together in a binding gel in an attempt to allow measurement of anions and cations in a single assay. Results from the MBL were compared to experiments performed using individual Chelex gels and ferrihydrite gels that have been shown to work successfully for DGT methodology. To facilitate combined analysis of P and cations by ICP-MS, HCl (1 M) was used for gel elution to minimize interferences from 14N16OH or 15N16O on 31P. All elements tested (Cd, Cu, Mn, Mo, P, and Zn) were bound successfully to the MBL. An elution efficiency of 0.92 was obtained for all elements, apart from Mo (0.79). This is higher than the elution efficiencies obtained previously for pure Chelex or ferrihydrite gels using HNO3 (1 M) as the eluent. Uptake of cations by DGT using the MBL was consistent across the pH range 5-9, which compares well with results using pure Chelex. Below pH 5, accumulated masses were lower for Mn, Cu, and Zn. Uptake of P and Mo was unaffected by pH in the range 3-8, and the amount absorbed compared well with results obtained previously for pure ferrihydrite gels. Performance of the MBL at different ionic strengths (0.001, 0.01 M) was comparable to performance using the pure Chelex gel. DGT measurements obtained using the MBL on agricultural soils correlated well (r2 = 0.95) with separate measurements obtained using either pure Chelex or ferrihydrite binding layers. This suggests that the MBL could be used for simultaneous measurement of cationic and anionic element availability in soils.

Biochemical characterization of the active heterodimer form of human heparanase (Hpa1) protein expressed in insect cells.

The mammalian endoglycosidase heparanase (Hpa1) is primarily responsible for cleaving heparan sulphate proteoglycans (HSPGs) present on the basement membrane of cells and its potential for remodelling the extracellular matrix (ECM) could be important in embryonic development and tumour metastasis. Elevated expression of this enzyme has been implicated in various pathological processes including tumour cell proliferation, metastasis, inflammation and angiogenesis. The enzyme therefore represents a potential therapeutic target. Hpa1 protein is initially synthesized as an inactive 65 kDa proenzyme that is then believed to be subsequently activated by proteolytic cleavage to generate an active heterodimer of 8 and 50 kDa polypeptides. By analysis of a series of Hpa1 deletion proteins we confirm that the 8 kDa subunit is essential for enzyme activity. We present here for the first time an insect cell expression system used for the generation of large amounts of recombinant protein of high specific activity. Individual subunits were cloned into baculoviral secretory vectors and co-expressed in insect cells. Active secreted heterodimer protein was recovered from the medium and isolated by a one-step heparin-Sepharose chromatography procedure to give protein of >90% purity. The recombinant enzyme behaved similarly to the native protein with respect to the size of HS fragments liberated on digestion, substrate cleavage specificity and its preference for acidic pH. A significant amount of activity, however, was also detectable at physiological pH values, as measured both by an in vitro assay and by in vivo degradation of cell-bound heparan sulphate.

Self-assembly of proteins and their nucleic acids.

We have developed an artificial protein scaffold, herewith called a protein vector, which allows linking of an in-vitro synthesised protein to the nucleic acid which encodes it through the process of self-assembly. This protein vector enables the direct physical linkage between a functional protein and its genetic code. The principle is demonstrated using a streptavidin-based protein vector (SAPV) as both a nucleic acid binding pocket and a protein display system. We have shown that functional proteins or protein domains can be produced in vitro and physically linked to their DNA in a single enzymatic reaction. Such self-assembled protein-DNA complexes can be used for protein cloning, the cloning of protein affinity reagents or for the production of proteins which self-assemble on a variety of solid supports. Self-assembly can be utilised for making libraries of protein-DNA complexes or for labelling the protein part of such a complex to a high specific activity by labelling the nucleic acid associated with the protein. In summary, self-assembly offers an opportunity to quickly generate cheap protein affinity reagents, which can also be efficiently labelled, for use in traditional affinity assays or for protein arrays instead of conventional antibodies.

Chemical speciation of Zn, Cd, Cu, and Pb in pore waters of agricultural and contaminated soils using Donnan dialysis.

Knowledge of trace metal speciation in soil pore waters is important in addressing metal bioavailability and risk assessment of contaminated soils. Numerous analytical methods have been utilized for determining trace metal speciation in aqueous environmental matrixes; however, most of these methods suffer from significant interferences. The Donnan dialysis membrane technique minimizes these interferences and has been used in this study to determine free Zn2+, Cd2+, Cu2+, and Pb2+ activities in pore waters from 15 agricultural and 12 long-term contaminated soils. The soils vary widely in their origin, pH, organic carbon content, and total metal concentrations. Pore water pM2+ activities also covered a wide range and were controlled by soil pH and total metal concentrations. For the agricultural soils, most of the free metal activities were below detection limit, apart from Zn2+ for which the fraction of free Zn2+ in soluble Zn ranged from 2.3 to 87% (mean 43%). Five of the agricultural soils had detectable free Cd2+ with fractions of free metal ranging from 59 to 102% (mean 75%). For the contaminated soils with detectable free metal concentrations, the fraction of free metal as a percentage of soluble metal varied from 9.9 to 97% (mean 50%) for Zn2+, from 22 to 86% (mean 49%) for Cd2+, from 0.4 to 32.1% (mean 5%) for Cu2+, and from 2.9 to 48.8% (mean 20.1%) for Pb2+. For the contaminated soils, the equilibrium speciation programs GEOCHEM and WHAM Model VI provided reasonable estimates of free Zn2+ fractions in comparison to the measured fractions (R2 approximately 0.7), while estimates of free Cd2+ fractions were less agreeable (R2 approximately 0.5). The models generally predicted stronger binding of Cu2+ to DOC and hence lower fractions of free Cu2+ as compared with the observed fractions. The binding of Cu2+ and Pb2+ to DOC predicted by WHAM Model VI was much strongerthan that predicted by GEOCHEM.