High-throughput genotyping with the GoldenGate assay in the complex genome of soybean

Large numbers of single nucleotide polymorphism (SNP) markers are now available for a number of crop species. However, the high-throughput methods for multiplexing SNP assays are untested in complex genomes, such as soybean, that have a high proportion of paralogous genes. The Illumina GoldenGate assay is capable of multiplexing from 96 to 1,536 SNPs in a single reaction over a 3-day period. We tested the GoldenGate assay in soybean to determine the success rate of converting verified SNPs into working assays. A custom 384-SNP GoldenGate assay was designed using SNPs that had been discovered through the resequencing of five diverse accessions that are the parents of three recombinant inbred line (RIL) mapping populations. The 384 SNPs that were selected for this custom assay were predicted to segregate in one or more of the RIL mapping populations. Allelic data were successfully generated for 89% of the SNP loci (342 of the 384) when it was used in the three RIL mapping populations, indicating that the complex nature of the soybean genome had little impact on conversion of the discovered SNPs into usable assays. In addition, 80% of the 342 mapped SNPs had a minor allele frequency >10% when this assay was used on a diverse sample of Asian landrace germplasm accessions. The high success rate of the GoldenGate assay makes this a useful technique for quickly creating high density genetic maps in species where SNP markers are rapidly becoming available. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Mention of a trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply approval of a product to the exclusion of others that may be suitable.     

Microbial biodiversity and in situ bioremediation of endosulfan contaminated soil

Molecular characterization based on 16s rDNA gene sequence analysis of bacterial colonies isolated from endosulfan contaminated soil showed the presence of Ochrobacterum sp, Burkholderia sp, Pseudomonas alcaligenes, Pseudomonas sp and Arthrobacter sp which degraded 57–90% of α-endosulfan and 74–94% of β-endosulfan after 7days. Whole cells of Pseudomonas sp and Pseudomonas alcaligenes showed 94 and 89% uptake of α-isomer and 86 and 89% of β-endosulfan respectively in 120 min. In Pseudomonas sp, endosulfan sulfate was the major metabolite detected during the degradation of α-isomer, with minor amount of endosulfan diol while in Pseudomonas alcaligenes endosulfan diol was the only product during α-endosulfan degradation. Whole cells of Pseudomonas sp also utilized 83% of endosulfan sulfate in 120 min. In situ applications of the defined consortium consisting of Pseudomonas alcaligenes and Pseudomonas sp (1:1) in plots contaminated with endosulfan showed that 80% of α-endosulfan and 65% of β-endosulfan was degraded after 12 weeks of incubation. Endosulfan sulfate formed during endosulfan degradation was subsequently degraded to unknown metabolites. ERIC-PCR analysis indicated 80% survival of introduced population of Pseudomonas alcaligenes and Pseudomonas sp in treated plots.     

Chelator-facilitated removal of iron from transferrin: relevance to combined chelation therapy

Current iron chelation therapy consists primarily of DFO (desferrioxamine), which has to be administered via intravenous infusion, together with deferiprone and deferasirox, which are orally-active chelators. These chelators, although effective at decreasing the iron load, are associated with a number of side effects. Grady suggested that the combined administration of a smaller bidentate chelator and a larger hexadentate chelator, such as DFO, would result in greater iron removal than either chelator alone [Grady, Bardoukas and Giardina (1998) Blood 92, 16b]. This in turn could lead to a decrease in the chelator dose required. To test this hypothesis, the rate of iron transfer from a range of bidentate HPO (hydroxypyridin-4-one) chelators to DFO was monitored. Spectroscopic methods were utilized to monitor the decrease in the concentration of the Fe-HPO complex. Having established that the shuttling of iron from the bidentate chelator to DFO does occur under clinically relevant concentrations of chelator, studies were undertaken to evaluate whether this mechanism of transfer would apply to iron removal from transferrin. Again, the simultaneous presence of both a bidentate chelator and DFO was found to enhance the rate of iron chelation from transferrin at clinically relevant chelator levels. Deferiprone was found to be particularly effective at 'shuttling' iron from transferrin to DFO, probably as a result of its small size and relative low affinity for iron compared with other analogous HPO chelators.     

Mixture design as first step for improved glutaminase production in solid-state fermentation by isolated Bacillus

Aim: Investigation of mixture‐design impact on glutaminase production by isolated Bacillus sp. Methods and Results: An augmented simplex centroid design was used to optimize a three (wheat bran, Bengal gram husk and palm seed fibre) component mixture for glutaminase production. Selected substrate materials showed impact on glutaminase production values at individual level by Bengal gram husk [2789 U gds^?1 (gram dry substrate] and in two‐level combination with wheat bran and Bengal gram husk (maximum of 3300 U gds^?1). Conclusion: Bengal gram husk is the most suitable substrate medium for glutaminase production by Bacillus sp. Maximum glutaminase production is achieved using solid‐substrate mixture at two‐level combinations in the ratio of 66 : 34 for Bengal gram husk and wheat bran, respectively. Significance and Impact of the Study: The present study has significance in large‐scale production of glutaminase at commercial level with the use of multi‐substrate rather than single‐substrate/support material.     

macroH2A1-dependent silencing of endogenous murine leukemia viruses

We show that macroH2A1 histone variants are important for repressing the expression of endogenous murine leukemia viruses (MLVs) in mouse liver. Intact MLV proviruses and proviruses with deletions in env were nearly silent in normal mouse liver and showed substantial derepression in macroH2A1 knockout liver. In contrast, MLV proviruses with a deletion in the 5′ end of pro-pol were expressed in normal liver and showed relatively low levels of derepression in knockout liver. macroH2A1 nucleosomes were enriched on endogenous MLVs, with the highest enrichment occurring on the 5′ end of pro-pol. The absence of macroH2A1 also led to a localized loss of DNA methylation on the 5′ ends of MLV proviruses. These results demonstrate that macroH2A1 histones have a significant role in silencing endogenous MLVs in vivo and suggest that specific internal MLV sequences are targeted by a macroH2A1-dependent silencing mechanism.     

Functional analysis of Fontan energy dissipation

We formalize the hydrodynamic energy dissipation in the total cavopulmonary connection (TCPC) using dimensional analysis and examine the effect of governing flow variables; namely, cardiac output, flow split, body surface area, Reynolds number, and certain geometric characteristics. A simplistic and clinically useful mathematical model of the dependence of energy dissipation on the governing variables is developed. In vitro energy loss data corresponding to six patients' anatomies validated the predicted dependency of each variable and was used to develop a predictive, semi-empirical energy dissipation model of the TCPC. It is shown that energy dissipation is a cubic function of pulmonary flow split in the physiological range. Furthermore, non-dimensional energy dissipation, which is a measure of resistance of the connection, is dependent on Reynolds number and geometrical factors alone. Non-dimensional energy dissipation decreases with Reynolds number as Re(-0.25) (R(2)>0.95). In addition, for high Reynolds numbers, within physiological exercise limits, dissipation strongly correlates to minimum PA area as a power law decay with an exponent of -5/4 (R(2)>0.88). This study presents a simple analytical form of energy dissipation rate in complex patient-specific TCPCs that accurately captures the effect of cardiac output, flow split, body surface area, Reynolds number, and pulmonary artery size within physiological limits. Further studies with larger sample sizes are necessary for incorporating finer geometrical parameters such as vessel curvatures and offsets.     

Structural simulations of prosthetic tri-leaflet aortic heart valves

This study presents a combined computational and experimental approach for the nonlinear structural simulations of polymeric tri-leaflet aortic valves (PAVs). Nonlinear shell-based and quasi-static finite-element (FE) structural models are generated for a prosthetic valve geometry that includes the leaflets, stents and root materials, such as the bottom base and outside walls. The PAV structural model is subject to an ensemble averaged transvalvular pressure waveform measured from repeated in vitro tests conducted with a left heart simulator. High-resolution optical measurements are used to measure the in vitro kinematics of the leaflets and the stents. Qualitative and quantitative deformation measures are defined in order to compare the predicted kinematics from the PAV models with the in vitro measurements. Six new quantitative deformation metrics are introduced. They include three distances measuring the current PAV geometric center to the leaflet edges while additional three distances define the stent post-to-stent post (SPTSP) distances. The structural model is able to predict the kinematic deformation metrics with maximum errors around 10% especially in systole where the displacements are larger in magnitude. The combined structural modeling with experimental simulations along with the new proposed deformation metrics provide an effective way to study the PAV structural behavior and a path for improving the structural design of prosthetic valves.     

Sodium arsenite induces heat shock protein 70 expression and protects against secretagogue-induced trypsinogen and NF-kappaB activation

Heat shock proteins (HSPs), induced by a variety of stresses, are known to protect against cellular injury. Recent studies have demonstrated that prior beta-adrenergic stimulation as well as thermal or culture stress induces HSP70 expression and protects against cerulein-induced pancreatitis. The goal of our current studies was to determine whether or not a non-thermal, chemical stressor like sodium arsenite also upregulates HSP70 expression in the pancreas and prevents secretagogue-induced trypsinogen and NF-kappaB activation. We examined the effects of sodium arsenite preadministration on the parameters of cerulein-induced pancreatitis in rats and then monitored the effects of preincubating pancreatic acini with sodium arsenite in vitro. Our results showed that sodium arsenite pretreatment induced HSP70 expression both in vitro and in vivo and significantly ameliorated the severity of cerulein-induced pancreatitis, as evidenced by the markedly reduced degree of hyperamylasemia, pancreatic edema, and acinar cell necrosis. Sodium arsenite pretreatment not only inhibited trypsinogen activation and the subcellular redistribution of cathepsin B, but also prevented NF-kappaB translocation to the nucleus by inhibiting the IkappaBalpha degradation both in vivo and in vitro. We also examined the effect of sodium arsenite pretreatment in a more severe model of pancreatitis induced by L-arginine and found a similarly protective effect. Based on our observations we conclude that, like thermal stress, chemical stressors such as sodium arsenite also induce HSP70 expression in the pancreas and protect against acute pancreatitis. Thus, non-thermal pharmacologically induced stress can help prevent or treat pancreatitis.