Design and testing of a humanized porcine donor for xenotransplantation.

Recent human decedent model studies1,2 and compassionate xenograft use3 have explored the promise of porcine organs for human transplantation. To proceed to human studies, a clinically ready porcine donor must be engineered and its xenograft successfully tested in nonhuman primates. Here we describe the design, creation and long-term life-supporting function of kidney grafts from a genetically engineered porcine donor transplanted into a cynomolgus monkey model. The porcine donor was engineered to carry 69 genomic edits, eliminating glycan antigens, overexpressing human transgenes and inactivating porcine endogenous retroviruses. In vitro functional analyses showed that the edited kidney endothelial cells modulated inflammation to an extent that was indistinguishable from that of human endothelial cells, suggesting that these edited cells acquired a high level of human immune compatibility. When transplanted into cynomolgus monkeys, the kidneys with three glycan antigen knockouts alone experienced poor graft survival, whereas those with glycan antigen knockouts and human transgene expression demonstrated significantly longer survival time, suggesting the benefit of human transgene expression in vivo. These results show that preclinical studies of renal xenotransplantation could be successfully conducted in nonhuman primates and bring us closer to clinical trials of genetically engineered porcine renal grafts.

Effects of conservation buffer systems on adsorption of fluorescent-labeled Escherichia coli.

The magnitude of bacterial transport through runoff into surface water or infiltration into groundwater is influenced by the adsorption processes in soil. The objective of this study was to evaluate fluorescent-labeled Escherichia coli (E. coli) adsorption by soil under agroforestry buffer (AB), grass buffer (GB), and row crop (RC) management. Adsorption experiments were conducted by inoculating three masses (0.5, 1, and 10 g) of each treatment (AB, GB, and RC) with E. coli O157:H7-GFP with concentration ranges of 105 -108 colony-forming units (cfu) ml-1 . Adsorption data were evaluated using Langmuir, Freundlich, and Temkin adsorption isotherm models. The Freundlich isotherm model described the observed data well for all treatments using the 10-g soil mass, with the R2 values closer to unity in all treatments. The Freundlich Kf parameter, an indicator of adsorption capacity, was higher for the AB treatment (9.93 cfu ml-1 ) compared with the GB and RC treatments (2.32 and 1.27 cfu ml-1 , respectively). The multiple pairwise comparisons test (Tukey test) of the Freundlich 1/nf parameter demonstrated a significant difference (p < .05) between the AB treatment and the RC and GB treatments. Similarly, the Kf values were significantly (p = .05) higher for the 10-g mass under the same test conditions, but no significant differences were observed in the 0.5- and 1-g masses. This study demonstrated that AB has a higher E. coli adsorption capacity and the potential for mitigating the effects of E. coli O157:H7 transport to surface or groundwater through the soil ecosystem.

Realizing cool and warm white-LEDs based on color controllable (Sr,Ba)2Al3O6F:Eu2+ phosphors obtained via a microwave-assisted diffusion method.

Globally, phosphor converted white-LEDs (W-LEDs) are among the most suitable sources to reduce energy consumption. Nevertheless, modernization of efficient broadband emitting phosphors is most crucial to improve the W-LED performance. Herein, we synthesized a series of novel broadband emitting Sr2-xAl3O6F:xEu2+ phosphors via a new microwave-assisted diffusion method. Rietveld refinement of the obtained X-ray diffraction results was performed to recognize the exact crystal phase and the various cationic sites. Oxygen vacancies (VO) formed under synthetic reducing conditions enabled Sr2Al3O6F to demonstrate bright self-activated bluish emission. Doping of Eu2+ ions unlocked the energy transfer process from the host to the activator ions, owing to which, the self-activated emission diminished and the Eu2+-doped sample showed amplified bluish-green emission. The gradual increase in Eu2+ concentrations regulated the controllable emissions from the bluish (0.34, 0.42) to the greenish (0.38, 0.43) zone under UV excitation. Because of the different absorption preferences of Eu2+ ions located at the different Sr2+ sites, Sr2-xAl3O6F:xEu2+ exhibited bluish-white emission under blue irradiation. A further enhancement in PL intensity had been observed by the cation substitution of Ba2+ for Sr2+ sites in the optimum Sr1.95Al3O6F:0.05Eu2+ phosphor. The as-fabricated W-LEDs utilizing the optimized Sr1.75Ba0.2Al3O6F:0.05Eu2+ phosphor exhibited a cool-white light emission along with a 372 nm NUV-LED and a 420 nm blue-LED with a moderate CRI of 70 and a CCT above 6000 K. Such cool white emission was controlled to natural white with the CCT close to 5000 K, and the CRI above 80 via utilizing a suitable red emitting phosphor. The W-LED performances of the optimized phosphor justified its applicability to produce white light for lighting applications.

Extensive use of waste glass in one-part alkali-activated materials: Towards sustainable construction practices.

The feasibility of the extensive recycling of waste glass in alkali-activated materials (AAMs) was evaluated. The waste glass was utilised in AAMs for two purposes: a partial activator and a mineral precursor. The waste glass was blended with commercial sodium hydroxide and then heated to produce the solid activator powder. The technical performance of waste glass-based activator was investigated to replace commercial sodium silicate, a common alkali-activator used in AAMs. The effect of waste glass using only as the activator (WGA) and using as both activator and precursor (WGAP) in fly ash/slag-based one-part AAMs was studied using strength and microstructure characterisations. A mass-cost and emission analysis of waste glass-based AAMs (WGA and WGAP) was conducted, comparing the results with ordinary Portland cement (OPC). Characterisation tests of waste glass-based activator showed the effective formation of sodium silicate minerals with the adequate dissolution of activator in water by releasing reactive alkali and silica. Both WGA and WGAP showed comparable strengths at 56 days with a denser microstructure under ambient curing. According to mass analysis, waste glass could be utilised up to 17% by mass of total binder. Based on the analysis of cost and CO2 emissions, WGA and WGAP are around 23% and 15% cheaper and 84% and 82% greener than OPC. The dual role of waste glass in AAMs as an activator and as a precursor broadens the recycling of glass waste in the cement industry by favouring technical and environmental outcomes.

Self-assembly and viscosity changes of binary surfactant solutions: A molecular dynamics study.

HYPOTHESIS: Structure and self-assembly of surfactants in the solution shows a fundamental influence on its viscosity. Through molecular simulations using Martini force field, synergistic effects in aggregation as well as the viscosity changes of a binary ionic surfactant system can be modelled. Simulations: Coarse-grained molecular dynamics simulations are performed to model the SDS/CAPB binary surfactant solution, and both equilibrium and non-equilibrium methods are used to calculate the viscosity of the equilibrated micellar systems. FINDINGS: Our simulation results indicate that the new version of the Martini force field can provide more reasonable self-assembly of surfactant, both single and binary system. Synergistic effects in micelle formation for SDS/CAPB have been successfully reproduced, that is, the formation of cylindrical micelles or even wormlike micelles at a lower concentration when compared with the pure system. Meanwhile, both equilibrium and non-equilibrium methods provide quantitatively comparable viscosity for each system. For pure micellar system, the viscosity linearly increases with the total concentration. Nevertheless, our simulation fails to capture the viscosity enhancement of the solution in corresponding with the formation of rodlike or wormlike micelles, and a full parameter optimization of force field is still necessary.

Different strategies of foam stabilization in the use of foam as a fracturing fluid.

An attractive alternative to mitigate the adverse effects of conventional water-based fluids on the efficiency of hydraulic fracturing is to inject foam-based fracking fluids into reservoirs. The efficiency of foaming fluids in subsurface applications largely depends on the stability and transportation of foam bubbles in harsh environments with high temperature, pressure and salinity, all of which inevitably lead to poor foam properties and thus limit fracturing efficiency. The aim of this paper is to elaborate popular strategies of foam stabilization under reservoir conditions. Specifically, this review first discusses three major mechanisms governing foam decay and summarizes recent progress in research on these phenomena. Since surfactants, polymers, nanoparticles and their composites are popular options for foam stabilization, their stabilizing effects, especially the synergies in composites, are also reviewed. In addition to reporting experimental results, the paper also reports recent advances in interfacial properties via molecular dynamical simulation, which provide new insights into gas/liquid interfacial properties under the influence of surfactants at molecular scale. The results of both experiments and simulations indicate that foam additives play an essential role in foam stability and the synergic effects of surfactants and nanoparticles exhibit more favorable performance.

Pore scale investigation on scaling-up micro-macro capillary number and wettability on trapping and mobilization of residual fluid.

The mobilization mechanism of the trapped phases controlled by the viscous force and capillary force in porous media is crucial to various engineering applications. In this paper, pore scale water flooding process in rock models with nonuniform wettability is simulated by computational fluid dynamics (CFD) using the volume of fluid (VOF) model. Four types of rock are imaged by micro-CT (µ-CT) and adopted as inputs to generate the structured mesh models. The simulations of two-phase flow are carried out to study the immiscible displacement process in the development of oil fields. The scaling-up critical capillary number at micro-macro scale are acquired and validated, the effects of which on relative permeability, residual oil recovery and immiscible displacement efficiency are analyzed. The simulation results indicate that the critical capillary number at microscopic scale ranges from 10-6 to 10-5 for water-wetted and oil-wetted rock respectively, and approaches to 1 at the macro scale. The effect of wettability on oil recovery is positive for intermediate-wetted or weak water-wetted rock, while negative for strong wettability.

Influence of agroforestry plant species on the infiltration of S-Metolachlor in buffer soils.

Agroforestry practices have been acknowledged for reducing pesticide losses while maintaining land productivity. Pesticide removal from overland flow results from great infiltration capacities of the buffer soils. This can in turn threaten the quality of groundwater in case of poor pesticide sorption and degradation in the root-influenced zone. These mechanisms and their balance are likely to be influenced by plant species. However, little is known about the role of agroforestry species in the infiltration of herbicides. The aim of this study was thereby to evaluate how popular agroforestry species modulate the infiltration of water and of a widely used herbicide. We established large buffer microcosms by planting Brome grass, Black walnut, Pin oak and Poplar trees in repacked soil columns. After a growth season of 4 months, we performed ponded infiltration experiments with bromide and S-Metolachlor. We used then the HYDRUS 1D model to compare the hydrodynamic properties and S-Metolachlor transport patterns between the microcosms. In addition, we compared the sorption properties of the rhizosphere and bulk soils. We found that the tree species increased the sorption of S-Metolachlor in soil with Kd being 3 times greater than in the un-vegetated and Brome grass microcosms. Poplar trees increased the hydraulic conductivity (Ksat) compared to the control and was associated to a low retardation of S-metolachlor, which increases the risk of groundwater contamination. With slightly reduced Ksat and retardation factor in the root zone, 1.6 to 1.8 times greater than in the control treatment, Black walnut appears as an optimal species for mitigating S-Metolachlor. The Brome grass and oak microcosms had the lowest Ksat of all treatments and S-Metolachlor retardation factors were equal and slightly increased compared to the control, respectively. These results show that agroforestry buffer's efficiency can be optimized by selecting appropriate species.

Development of PLEAD: A Database Containing Event-based Runoff Phosphorus Loadings from Agricultural Fields.

Computer models are commonly used for predicting risks of runoff P loss from agricultural fields by enabling simulation of various management practices and climatic scenarios. For P loss models to be useful tools, however, they must accurately predict P loss for a wide range of climatic, physiographic, and land management conditions. A complicating factor in developing and evaluating P loss models is the relative scarcity of available measured field data that adequately capture P losses before and after implementing management practices in a variety of physiographic settings. Here, we describe the development of the P Loss in runoff Events from Agricultural fields Database (PLEAD)-a compilation of event-based, field-scale dissolved and/or total P loss runoff loadings from agricultural fields collected at various research sites located in the US Heartland and southern United States. The database also includes runoff and erosion rates; soil-test P; tillage practices; planting and harvesting rates and practices; fertilizer application rate, method, and timing; manure application rate, method, and timing; and livestock grazing density and timing. In total, >1800 individual runoff events-ranging in duration from 0.4 to 97 h-have been included in the database. Event runoff P losses ranged from <0.05 to 1.3 and 3.0 kg P ha for dissolved and total P, respectively. The data contained in this database have been used in multiple research studies to address important modeling questions relevant to P management planning. We provide these data to encourage additional studies by other researchers. The PLEAD database is available at .

CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles.

Harnessing CRISPR-Cas9 technology provides an unprecedented ability to modify genomic loci via DNA double-strand break (DSB) induction and repair. We analyzed nonhomologous end-joining (NHEJ) repair induced by Cas9 in budding yeast and found that the orientation of binding of Cas9 and its guide RNA (gRNA) profoundly influences the pattern of insertion/deletions (indels) at the site of cleavage. A common indel created by Cas9 is a 1-bp (+1) insertion that appears to result from Cas9 creating a 1-nt 5' overhang that is filled in by a DNA polymerase and ligated. The origin of +1 insertions was investigated by using two gRNAs with PAM sequences located on opposite DNA strands but designed to cleave the same sequence. These templated +1 insertions are dependent on the X-family DNA polymerase, Pol4. Deleting Pol4 also eliminated +2 and +3 insertions, which are biased toward homonucleotide insertions. Using inverted PAM sequences, we also found significant differences in overall NHEJ efficiency and repair profiles, suggesting that the binding of the Cas9:gRNA complex influences subsequent NHEJ processing. As with events induced by the site-specific HO endonuclease, CRISPR-Cas9-mediated NHEJ repair depends on the Ku heterodimer and DNA ligase 4. Cas9 events are highly dependent on the Mre11-Rad50-Xrs2 complex, independent of Mre11's nuclease activity. Inspection of the outcomes of a large number of Cas9 cleavage events in mammalian cells reveals a similar templated origin of +1 insertions in human cells, but also a significant frequency of similarly templated +2 insertions.

Assessment of dynamic material properties of intact rocks using seismic wave attenuation: an experimental study.

The mechanical properties of any substance are essential facts to understand its behaviour and make the maximum use of the particular substance. Rocks are indeed an important substance, as they are of significant use in the energy industry, specifically for fossil fuels and geothermal energy. Attenuation of seismic waves is a non-destructive technique to investigate mechanical properties of reservoir rocks under different conditions. The attenuation characteristics of five different rock types, siltstone, shale, Australian sandstone, Indian sandstone and granite, were investigated in the laboratory using ultrasonic and acoustic emission instruments in a frequency range of 0.1-1 MHz. The pulse transmission technique and spectral ratios were used to calculate the attenuation coefficient (α) and quality factor (Q) values for the five selected rock types for both primary (P) and secondary (S) waves, relative to the reference steel sample. For all the rock types, the attenuation coefficient was linearly proportional to the frequency of both the P and S waves. Interestingly, the attenuation coefficient of granite is more than 22% higher than that of siltstone, sandstone and shale for both P and S waves. The P and S wave velocities were calculated based on their recorded travel time, and these velocities were then used to calculate the dynamic mechanical properties including elastic modulus (E), bulk modulus (K), shear modulus (µ) and Poisson's ratio (ν). The P and S wave velocities for the selected rock types varied in the ranges of 2.43-4.61 km s-1 and 1.43-2.41 km h-1, respectively. Furthermore, it was observed that the P wave velocity was always greater than the S wave velocity, and this confirmed the first arrival of P waves to the sensor. According to the experimental results, the dynamic E value is generally higher than the static E value obtained by unconfined compressive strength tests.

Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats.

Trinucleotide repeats are a source of genome instability, causing replication fork stalling, chromosome fragility, and impaired repair. Specialized helicases play an important role in unwinding DNA structures to maintain genome stability. The Srs2 helicase unwinds DNA hairpins, facilitates replication, and prevents repeat instability and fragility. However, since Srs2 is a multifunctional protein with helicase activity and the ability to displace Rad51 recombinase, it was unclear which functions were required for its various protective roles. Here, using SRS2 separation-of-function alleles, we show that in the absence of Srs2 recruitment to PCNA or in helicase-deficient mutants, breakage at a CAG/CTG repeat increases. We conclude that Srs2 interaction with PCNA allows the helicase activity to unwind fork-blocking CAG/CTG hairpin structures to prevent breaks. Independently of PCNA binding, Srs2 also displaces Rad51 from nascent strands to prevent recombination-dependent repeat expansions and contractions. By 2D gel electrophoresis, we detect two different kinds of structured intermediates or joint molecules (JMs). Some JMs are Rad51-independent and exhibit properties of reversed forks, including being processed by the Exo1 nuclease. In addition, in a helicase-deficient mutant, Rad51-dependent JMs are detected, probably corresponding to recombination between sisters. These results clarify the many roles of Srs2 in facilitating replication through fork-blocking hairpin lesions.

Multisite Evaluation of APEX for Water Quality: I. Best Professional Judgment Parameterization.

The Agricultural Policy Environmental eXtender (APEX) model is capable of estimating edge-of-field water, nutrient, and sediment transport and is used to assess the environmental impacts of management practices. The current practice is to fully calibrate the model for each site simulation, a task that requires resources and data not always available. The objective of this study was to compare model performance for flow, sediment, and phosphorus transport under two parameterization schemes: a best professional judgment (BPJ) parameterization based on readily available data and a fully calibrated parameterization based on site-specific soil, weather, event flow, and water quality data. The analysis was conducted using 12 datasets at four locations representing poorly drained soils and row-crop production under different tillage systems. Model performance was based on the Nash-Sutcliffe efficiency (NSE), the coefficient of determination () and the regression slope between simulated and measured annualized loads across all site years. Although the BPJ model performance for flow was acceptable (NSE = 0.7) at the annual time step, calibration improved it (NSE = 0.9). Acceptable simulation of sediment and total phosphorus transport (NSE = 0.5 and 0.9, respectively) was obtained only after full calibration at each site. Given the unacceptable performance of the BPJ approach, uncalibrated use of APEX for planning or management purposes may be misleading. Model calibration with water quality data prior to using APEX for simulating sediment and total phosphorus loss is essential.

Multisite Evaluation of APEX for Water Quality: II. Regional Parameterization.

Phosphorus (P) Index assessment requires independent estimates of long-term average annual P loss from fields, representing multiple climatic scenarios, management practices, and landscape positions. Because currently available measured data are insufficient to evaluate P Index performance, calibrated and validated process-based models have been proposed as tools to generate the required data. The objectives of this research were to develop a regional parameterization for the Agricultural Policy Environmental eXtender (APEX) model to estimate edge-of-field runoff, sediment, and P losses in restricted-layer soils of Missouri and Kansas and to assess the performance of this parameterization using monitoring data from multiple sites in this region. Five site-specific calibrated models (SSCM) from within the region were used to develop a regionally calibrated model (RCM), which was further calibrated and validated with measured data. Performance of the RCM was similar to that of the SSCMs for runoff simulation and had Nash-Sutcliffe efficiency (NSE) > 0.72 and absolute percent bias (|PBIAS|) < 18% for both calibration and validation. The RCM could not simulate sediment loss (NSE < 0, |PBIAS| > 90%) and was particularly ineffective at simulating sediment loss from locations with small sediment loads. The RCM had acceptable performance for simulation of total P loss (NSE > 0.74, |PBIAS| < 30%) but underperformed the SSCMs. Total P-loss estimates should be used with caution due to poor simulation of sediment loss. Although we did not attain our goal of a robust regional parameterization of APEX for estimating sediment and total P losses, runoff estimates with the RCM were acceptable for P Index evaluation.

Congenital third nerve palsy with synergistic depression on attempted adduction and trigemino-oculomotor synkinesis: Underpinnings of a spectral dysinnervation disorder.

The authors describe a case of congenital partial pupil-sparing third cranial nerve palsy with absent adduction, synergistic depression of globe and widening of palpebral fissure on attempted adduction and synergistic elevation and adduction on mouth opening and sideways thrusting of jaw. The case illustrates trigemino-oculomotor synkinesis associated with congenital third nerve palsy. The possible mechanism of miswiring involving the medial longitudinal fasciculus and trigeminal nuclei is discussed. At least some cases of congenital third cranial nerve palsy may fall in the realm of congenital cranial dysinnervation disorders (CCDDs) sharing a much wider spectrum of presentation.

Association of FTO and near MC4R variants with obesity measures in urban and rural dwelling Sri Lankans.

OBJECTIVES: To investigate the association between the fat mass and obesity related (FTO) gene rs9939609 and near melanocortin-4-receptor (MC4R) gene rs17782313 polymorphisms with obesity measures and metabolic parameters in urban and rural dwelling Sri Lankans. METHODS: 535 subjects (60.9% female) from the general adult population (ages 18-70 years) representative of both urban (28.4%) and rural areas of residence were recruited by multi-stage random sampling. Body mass index (BMI), waist circumference (WC) and waist-to-hip ratio (WHR) was obtained by standard methods. DNA extracted from whole blood was genotyped using real-time PCR. RESULTS: The FTO risk genotypes (AA+AT) were associated with higher BMI (p=0.03) and WC (p=0.05) measures as well as categorical obesity (BMI ≥27.5kgm-2 definition) (OR 1.69 95% CI 1.11-2.56, p=0.01). The near MC4R risk genotypes (CC+CT) were associated with greater BMI (p=0.03) as well as categorical obesity (BMI ≥25kgm-2 definition) (OR 1.57 95% CI 1.11-2.22, p=0.01). In addition the MC4R risk genotype carriers (CC+CT) had significantly higher fasting blood sugar (FBS) levels compared to the 'TT' genotype carriers independent of BMI (p=0.05). Urban living was associated with significantly greater BMI values for FTO risk genotypes compared to rural living (p=0.02). CONCLUSIONS: FTO and near MC4R variants are associated with obesity measures in Sri Lankan populations whilst urban living accentuates the obesogenic effect of the FTO polymorphism.

MTE1 Functions with MPH1 in Double-Strand Break Repair.

Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair.