RNAi-microsponges form through self-assembly of the organic and inorganic products of transcription

Inorganic nanostructures have been used extensively to package nucleic acids into forms useful for therapeutic applications. Here we report that the two products of transcription, RNA and inorganic pyrophosphate, can self-assemble to form composite microsponge structures composed of nanocrystalline magnesium pyrophosphate sheets (Mg₂P₂O₇•3.5H₂O) with RNA adsorbed to their surfaces. The microsponge particles contain high loadings of RNA (15-21 wt.%) that are protected from degradation and can be obtained through a rolling circle mechanism as large concatemers capable of mediating RNAi. The morphology of the RNAi microsponges is influenced by the time-course of the transcription reaction and interactions between RNA and the inorganic phase. Previous work demonstrated that polycations can be used to condense RNAi microsponges into nanoparticles capable of efficient transfection with low toxicity. Our new findings suggest that the formation of these nanoparticles is mediated by the gradual dissolution of magnesium pyrophosphate that occurs in the presence of polycations. The simple one-pot approach for assembling RNAi microsponges along with their unique properties could make them useful for RNA-based therapeutics.

'Click cyclic ADP-ribose': a neutral second messenger mimic

Analogues of the potent Ca(2+) releasing second messenger cyclic ADP-ribose (cADPR) with a 1,2,3-triazole pyrophosphate bioisostere were synthesised by click-mediated macrocyclisation. The ability to activate Ca(2+) release was surprisingly retained, and hydrolysis of cADPR by CD38 could also be inhibited, illustrating the potential of this approach to design drug-like signalling pathway modulators.

Analysis of enzyme activities

The evaluation of enzyme activities, especially their capacities, represents an important step towards the modelling of biochemical pathways in living organisms. The implementation of microplate technology enables the determination of up to >50 enzymes in relatively large numbers of samples and in various biological materials. Most of these enzymes are involved in central metabolism and several pathways are entirely covered. Direct or indirect assays can be used, as well as highly sensitive assays, depending on the abundance of the enzymes under study. To exemplify such methods, protocols for UDP-glucose pyrophosphorylase (E.C. 2.7.7.9) operating in real time and for pyrophosphate:fructose-6-phosphate 1-phosphotransferase (E.C. 2.7.1.90) are presented.

Oxidative UO2 dissolution induced by soluble Mn(III)

The stability of UO2 is critical to the success of reductive bioremediation of uranium. When reducing conditions are no longer maintained, Mn redox cycling may catalytically mediate the oxidation of UO2 and remobilization of uranium. Ligand-stabilized soluble Mn(III) was recently recognized as an important redox-active intermediate in Mn biogeochemical cycling. This study evaluated the kinetics of oxidative UO2 dissolution by soluble Mn(III) stabilized by pyrophosphate (PP) and desferrioxamine B (DFOB). The Mn(III)-PP complex was a potent oxidant that induced rapid UO2 dissolution at a rate higher than that by a comparable concentration of dissolved O2. However, the Mn(III)-DFOB complex was not able to induce oxidative dissolution of UO2. The ability of Mn(III) complexes to oxidize UO2 was probably determined by whether the coordination of Mn(III) with ligands allowed the attachment of the complexes to the UO2 surface to facilitate electron transfer. Systematic investigation into the kinetics of UO2 oxidative dissolution by the Mn(III)-PP complex suggested that Mn(III) could directly oxidize UO2 without involving particulate Mn species (e.g., MnO2). The expected 2:1 reaction stoichiometry between Mn(III) and UO2 was observed. The reactivity of soluble Mn(III) in oxidizing UO2 was higher at lower ratios of pyrophosphate to Mn(III) and lower pH, which is probably related to differences in the ligand-to-metal ratio and/or protonation states of the Mn(III)-pyrophosphate complexes. Disproportionation of Mn(III)-PP occurred at pH 9.0, and the oxidation of UO2 was then driven by both MnO2 and soluble Mn(III). Kinetic models were derived that provided excellent fits of the experimental results.

The effect of composition on mechanical properties of brushite cements

Due to a fast setting reaction, good biological properties, and easily available starting materials, there has been extensive research within the field of brushite cements as bone replacing material. However, the fast setting of brushite cement gives them intrinsically low mechanical properties due to the poor crystal compaction during setting. To improve this, many additives such as citric acid, pyrophosphates, and glycolic acid have been added to the cement paste to retard the crystal growth. Furthermore, the incorporation of a filler material could improve the mechanical properties when used in the correct amounts. In this study, the effect of the addition of the two retardants, disodium dihydrogen pyrophosphate and citric acid, together with the addition of β-TCP filler particles, on the mechanical properties of a brushite cement was investigated. The results showed that the addition of low amounts of a filler (up to 10%) can have large effects on the mechanical properties. Furthermore, the addition of citric acid to the liquid phase makes it possible to use lower liquid-to-powder ratios (L/P), which strongly affects the strength of the cements. The maximal compressive strength (41.8MPa) was found for a composition with a molar ratio of 45:55 between monocalcium phosphate monohydrate and beta-tricalcium phosphate, an L/P of 0.25ml/g and a citric acid concentration of 0.5M in the liquid phase.

Determination of phosphate phases in sewage sludge ash-based fertilizers by Raman microspectroscopy

The chemical form of phosphate phases in sewage sludge ash (SSA)-based fertilizers was determined by Raman microspectroscopy. Raman mapping with a lateral resolution of 5 × 5 μm(2) easily detected different compounds present in the fertilizers with the help of recorded reference spectra of pure substances. Quartz and aluminosilicates showed Raman bands in the range of 450-520 cm(-1). Phosphates with apatite structure and magnesium triphosphate were determined at around 960 and 980 cm(-1), respectively. Furthermore, calcium/magnesium pyrophosphates were detected in some samples.

Effects of pH on the production of phosphate and pyrophosphate by matrix vesicles' biomimetics

During endochondral bone formation, chondrocytes and osteoblasts synthesize and mineralize the extracellular matrix through a process that initiates within matrix vesicles (MVs) and ends with bone mineral propagation onto the collagenous scaffold. pH gradients have been identified in the growth plate of long bones, but how pH changes affect the initiation of skeletal mineralization is not known. Tissue-nonspecific alkaline phosphatase (TNAP) degrades extracellular inorganic pyrophosphate (PPi), a mineralization inhibitor produced by ectonucleotide pyrophosphatase/phosphodiesterase-1 (NPP1), while contributing Pi from ATP to initiate mineralization. TNAP and NPP1, alone or combined, were reconstituted in dipalmitoylphosphatidylcholine liposomes to mimic the microenvironment of MVs. The hydrolysis of ATP, ADP, AMP, and PPi was studied at pH 8 and 9 and compared to the data determined at pH 7.4. While catalytic efficiencies in general were higher at alkaline pH, PPi hydrolysis was maximal at pH 8 and indicated a preferential utilization of PPi over ATP at pH 8 versus 9. In addition, all proteoliposomes induced mineral formation when incubated in a synthetic cartilage lymph containing 1 mM ATP as substrate and amorphous calcium phosphate or calcium-phosphate-phosphatidylserine complexes as nucleators. Propagation of mineralization was significantly more efficient at pH 7.5 and 8 than at pH 9. Since a slight pH elevation from 7.4 to 8 promotes considerably more hydrolysis of ATP, ADP, and AMP primarily by TNAP, this small pH change facilitates mineralization, especially via upregulated PPi hydrolysis by both NPP1 and TNAP, further elevating the Pi/PPi ratio, thus enhancing bone mineralization.

Pyrosequencing for microbial identification and characterization

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

A luminol chemiluminescence method for sensing histidine and lysine using enzyme reactions

The analysis of free amino acids in urine and plasma is useful for estimating disease status in clinical diagnoses. Changes in the concentration of free amino acids in foods are also useful markers of freshness, nutrition, and taste. In this study, the specific interaction between aminoacyl-tRNA synthetase (aaRS) and its corresponding amino acid was used to measure amino acid concentrations. Pyrophosphate released by the amino acid-aaRS binding reaction was detected by luminol chemiluminescence; the method provided selective quantitation of 1.0-30 μM histidine and 1.0-60 μM lysine.

Mechanistic studies on regioselective dephosphorylation of phosphate prodrugs during a facile synthesis of antitumor phosphorylated 2-phenyl-6,7-methylenedioxy-1H-quinolin-4-one

Phosphorylation of 2-(3-hydroxy-5-methoxyphenyl)-6,7-methylenedioxy-1H-quinolin-4-one (1) afforded diphosphate 2. We found that, upon treatment with methanol under mild conditions, 2 can undergo facile and highly regioselective dephosphorylation to give the monophosphate 3, with a phosphate group remaining on the phenyl ring. The details of the dephosphorylation process were postulated and then probed by LC-MS and HPLC analyses. Furthermore, as a preliminary study, the water soluble monophosphate prodrug 4 was tested for antitumor activity against a MCF-7 xenograft nude mice model.

The effect of amorphous pyrophosphate on calcium phosphate cement resorption and bone generation

Pyrophosphate ions are both inhibitors of HA formation and substrates for phosphatase enzymes. Unlike polyphosphates their hydrolysis results simultaneously in the complete loss of mineral formation inhibition and a localised elevation in orthophosphate ion concentration. Despite recent advances in our knowledge of the role of the pyrophosphate ion, very little is known about the effects of pyrophosphate on bone formation and even less is known about its local delivery. In this work we first developed a self setting pyrophosphate based calcium cement system with appropriate handling properties and then compared its in vivo degradation properties with those of a non-pyrophosphate containing control. Contrary to expectation, the presence of the pyrophosphate phase in the cement matrix did not inhibit mineralisation of the healing bone around the implant, but actually appeared to stimulate it. In vitro evidence suggested that enzymatic action accelerated dissolution of the inorganic pyrophosphate ions, causing a simultaneous loss of their mineralisation inhibition and a localised rise in supersaturation with respect to HA. This is thought to be a rare example of a biologically responsive inorganic material and these materials seem to be worthy of further investigation. Bioceramics to date have mainly been limited to orthophosphate, silicate and carbonate salts of calcium, here we report the successful application of a pyrophosphate material as a degradable osteoconductive bone repair cement.

A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase

The dynamics of the PPi release during the transcription elongation of bacterial RNA polymerase and its effects on the Trigger Loop (TL) opening motion are still elusive. Here, we built a Markov State Model (MSM) from extensive all-atom molecular dynamics (MD) simulations to investigate the mechanism of the PPi release. Our MSM has identified a simple two-state mechanism for the PPi release instead of a more complex four-state mechanism observed in RNA polymerase II (Pol II). We observed that the PPi release in bacterial RNA polymerase occurs at sub-microsecond timescale, which is ∼3-fold faster than that in Pol II. After escaping from the active site, the (Mg-PPi)(2-) group passes through a single elongated metastable region where several positively charged residues on the secondary channel provide favorable interactions. Surprisingly, we found that the PPi release is not coupled with the TL unfolding but correlates tightly with the side-chain rotation of the TL residue R1239. Our work sheds light on the dynamics underlying the transcription elongation of the bacterial RNA polymerase.

Structural insight into inositol pyrophosphate turnover

The diphosphoinositol polyphosphates ("inositol pyrophosphates"; PP-InsPs) regulate many cellular processes in eukaryotes, including stress responses, apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, telomere maintenance, insulin signaling and neutrophil activation. Thus, the enzymes that control the metabolism of the PP-InsPs serve important cell signaling roles. In order to fully characterize how these enzymes are regulated, we need to determine the atomic-level architecture of their active sites. Only then can we fully appreciate reaction mechanisms and their modes of regulation. In this review, we summarize published information obtained from the structural analysis of a human diphosphoinositol polyphosphate phosphohydrolase (DIPP), and a human diphosphoinositol polyphosphate kinase (PPIP5K). This work includes the analysis of crystal complexes with substrates, products, transition state analogs, and a novel phosphonoacetate substrate analog.

[In situ immobilization of Pb and Cd in orchard soil using soil ameliorants]

In situ immobilization of Pb and Cd in soil of two gardens in Golden Orchard of Chongqing was studied using soil ameliorants, which included eight treatments: control, quicklime, superphosphate, organic manure, quicklime + superphosphate, quicklime + organic manure, superphosphate + organic manure, and quicklime + superphosphate + organic manure. The results showed that all ameliorant treatments could decrease soil acidity in both the loquat garden and peach garden except the superphosphate treatment. Compared with the control, the soil pH in the two gardens increased by 0. 93 and 0. 79 with quicklime treatment for 120 d, respectively. Ameliorant treatments could decrease the bioavailability of Pb and Cd in the soil, and thus reduce the contents of Pb and Cd in the fruits. The available Pb contents in the soil of loquat garden and peach garden significantly decreased after the 150 d treatment with quicklime and superphosphate, by 3.46% and 3.56%, respectively, and the Pb contents in loquat and peach decreased by 18.3% and 14.44%, respectively. The available Cd content in the soil of loquat garden decreased by 10. 95% after the 150 d treatment with quicklime. The available Cd content in the soil of peach garden decreased by 7.09% after the 150 d treatment with quicklime, superphosphate and organic manure. Ameliorant treatments could further decrease the Cd content in loquat, and the Cd contents in loquat and peach decreased by 30.91% and 24.62% with quicklime treatment, respectively.

Functional analysis and molecular docking identify two active short-chain prenyltransferases in the green peach aphid, Myzus persicae

Short-chain prenyltransferases are responsible for biosynthesis of the C(10)-C(20) precursors of a variety of isoprenoids. We previously isolated two different short-chain prenyltransferases from the green peach aphid, Myzus persicae (MpIPPS1 and MpIPPS2). In this study, the activity of the two aphid prenyltransferases was analyzed in vitro. Kinetic analysis using recombinant enzymes showed that both prenyltransferases could efficiently catalyze the formation of C(10) geranyl diphosphate (GPP) and C(15) farnesyl diphosphate (FPP) from the C(5) substrates isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), and MpIPPS2 had higher catalytic activity than MpIPPS1. Product analysis by gas chromatography-mass spectrometry demonstrated that FPP was generated as the major product, but GPP could be detected at low enzyme concentrations. Molecular docking revealed that MpIPPS2 had higher binding affinity with the substrates DMAPP, IPP, and GPP than MpIPPS1, which supported the experimentally determined kinetic parameters. Molecular docking also identified an amino acid residue (K266) critical to the catalytic activity of both MpIPPS1 and MpIPPS2. This prediction was subsequently confirmed by site-directed mutagenesis, in which a point mutation (K266I) abolished the activity of both MpIPPS1 and MpIPPS2. Our data illustrate that both aphid short-chain prenyltransferases are active forms, which is in contrast to the previously reported results.

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

Human DNA Pol κ is a polymerase enzyme, specialized for near error-free bypass of certain bulky chemical lesions to DNA that are derived from environmental carcinogens present in tobacco smoke, automobile exhaust and cooked food. By employing ab initio QM/MM-MD (Quantum Mechanics/Molecular Mechanics-Molecular Dynamics) simulations with umbrella sampling, we have determined the entire free energy profile of the nucleotidyl transfer reaction catalyzed by Pol κ and provided detailed mechanistic insights. Our results show that a variant of the Water Mediated and Substrate Assisted (WMSA) mechanism that we previously deduced for Dpo4 and T7 DNA polymerases is preferred for Pol κ as well, suggesting its broad applicability. The hydrogen on the 3'-OH primer terminus is transferred through crystal and solvent waters to the γ-phosphate of the dNTP, followed by the associative nucleotidyl transfer reaction; this is facilitated by a proton transfer from the γ-phosphate to the α,β-bridging oxygen as pyrophosphate leaves, to neutralize the evolving negative charge. MD simulations show that the near error-free incorporation of dCTP opposite the major benzo[a]pyrene-derived dG lesion is compatible with the WMSA mechanism, allowing for an essentially undisturbed pentacovalent phosphorane transition state, and explaining the bypass of this lesion with little mutation by Pol κ.

Effects of reed straw, zeolite, and superphosphate amendments on ammonia and greenhouse gas emissions from stored duck manure

Stored poultry manure can be a significant source of ammonia (NH) and greenhouse gases (GHGs), including nitrous oxide (NO), methane (CH), and carbon dioxide (CO) emissions. Amendments can be used to modify physiochemical properties of manure, thus having the potential to reduce gas emissions. Here, we lab-tested the single and combined effects of addition of reed straw, zeolite, and superphosphate on gas emissions from stored duck manure. We showed that, over a period of 46 d, cumulative NH emissions were reduced by 61 to 70% with superphosphate additions, whereas cumulative NO emissions were increased by up to 23% compared with the control treatment. Reed straw addition reduced cumulative NH, NO, and CH emissions relative to the control by 12, 27, and 47%, respectively, and zeolite addition reduced cumulative NH and NO emissions by 36 and 20%, respectively. Total GHG emissions (as CO-equivalents) were reduced by up to 27% with the additions of reed straw and/or zeolite. Our results indicate that reed straw or zeolite can be recommended as amendments to reduce GHG emissions from duck manure; however, superphosphate is more effective in reducing NH emissions.

Influence of amendments on soil arsenic fractionation and phytoavailability by Pteris vittata L

Increasing availability of soil arsenic is of significance for accelerating phytoremediation efficiency of As-polluted sites. The effects of seven amendments, i.e., citrate, oxalate, EDTA, sodium polyacrylate (SPA), phosphate rock (PR), single superphosphate (SSP), and compost on fractionation and phytoavailability of soil As were investigated in lab culture experiment. The results showed that the addition of PR, SPA, EDTA or compost to soils significantly increased the concentration of NaHCO(3)-extractable As over a 120 d incubation period compared with the control (amendment-free) soil. Then, the four amendments were selected to add to As-contaminated soil growing Pteris vittata. It was concluded that As accumulation by the fern increased significantly under the treatments of PR and SPA by 25% and 31%, respectively. For As fractionation in soil, SPA increased Fe-As significantly by 51% and PR increased Ca-As significantly by 18%, while both the two amendments reduced occluded-As by 16% and 19%, respectively. Adding PR and SPA in soil increased the activities of urease and neutral phosphatase resulting from the improvement the fertility and physical structure of the soil, which benefits plant growth and As absorption of P. vittata. The results of the research revealed that both PR and SPA were effective amendments for improving phytoremediation of As-contaminated sites by P. vittata.

Catalysis and sulfa drug resistance in dihydropteroate synthase

The sulfonamide antibiotics inhibit dihydropteroate synthase (DHPS), a key enzyme in the folate pathway of bacteria and primitive eukaryotes. However, resistance mutations have severely compromised the usefulness of these drugs. We report structural, computational, and mutagenesis studies on the catalytic and resistance mechanisms of DHPS. By performing the enzyme-catalyzed reaction in crystalline DHPS, we have structurally characterized key intermediates along the reaction pathway. Results support an S(N)1 reaction mechanism via formation of a novel cationic pterin intermediate. We also show that two conserved loops generate a substructure during catalysis that creates a specific binding pocket for p-aminobenzoic acid, one of the two DHPS substrates. This substructure, together with the pterin-binding pocket, explains the roles of the conserved active-site residues and reveals how sulfonamide resistance arises.

Modified Fenton oxidation of polycyclic aromatic hydrocarbon (PAH)-contaminated soils and the potential of bioremediation as post-treatment

This work focuses on the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil using modified Fenton (MF) treatment coupled with a novel chelating agent (CA), a more effective technique among currently available technologies. The performance of MF treatment to promote PAH oxidation in artificially contaminated soil was investigated in a packed column with a hydrogen peroxide (H(2)O(2)) delivery system simulating in-situ soil flushing which is more representative of field conditions. The effectiveness of process parameters H(2)O(2)/soil, Fe(3+)/soil, CA/soil weight ratios and reaction time were studied using a 2(4) three level factorial design experiments. An optimised operating condition of the MF treatment was observed at H(2)O(2)/soil 0.05, Fe(3+)/soil 0.025, CA/soil 0.04 and 3h reaction time with 79.42% and 68.08% PAH removals attainable for the upper and lower parts of the soil column respectively. The effects of natural attenuation and biostimulation process as post-treatment in the remediation of the PAH-contaminated soil were also studied. In all cases, 3-aromatic ring PAH (phenanthrene) was more readily degraded than 4-aromatic ring PAH (fluoranthene) regardless of the bioremediation approach. The results revealed that both natural attenuation and biostimulation could offer remarkable enhancement of up to 6.34% and 9.38% in PAH removals respectively after 8 weeks of incubation period. Overall, the results demonstrated that combined inorganic CA-enhanced MF treatment and bioremediation serves as a suitable strategy to enhance soil quality particularly to remediate soils heavily contaminated with mixtures of PAHs.

[Non-hydrolysable analogs of inorganic pyrophosphate as inhibitors of hepatitis C virus RNA-dependent RNA-polymerase]

Inorganic pyrophosphate (PPi) is a product of the polymerization reaction catalyzed by DNA- and RNA-polymerases. We have synthesized a number of novel non-hydrolysable PPi analogues, some of them have demonstrated inhibition of polymerization reaction catalyzed by hepatitis C virus RNA-dependent RNA-polymerase (NS5B). A new pharmacophore has been developed based on non-hydrolysable methylene-diphosphonate backbone. Structure-activity relationship analysis of 12 bisphosphonates is presented and structural features crucial for the ability of molecule to inhibit NS5B polymerase activity are ascertained.

Nonradioactive assay for detecting isoprenyl diphosphate synthase activity in crude plant extracts using liquid chromatography coupled with tandem mass spectrometry

Terpenoids form the largest class of plant metabolites involved in primary and secondary metabolism. Isoprenyl diphosphate synthases (IDSs) catalyze the condensation of the C(5) terpenoid building blocks, isopentenyl diphosphate and dimethylallyl diphosphate, to form geranyl diphosphate (C(10)), farnesyl diphosphate (C(15)), and geranylgeranyl diphosphate (C(20)). These branch point reactions control the flow of metabolites that act as precursors to each of the major terpene classes-monoterpenes, sequiterpenes, and diterpenes, respectively. Thus accurate and easily performed assays of IDS enzyme activity are critical to increase our knowledge about the regulation of terpene biosynthesis. Here we describe a new and sensitive nonradioactive method for carrying out IDS assays using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to detect the short-chain prenyl diphosphate products directly without dephosphorylation. Furthermore, we were able to separate cisoid and transoid isomers of both C(10) enzyme products (geranyl diphosphate and neryl diphosphate) and three C(15) products [(E,E)-, (Z,E)-, and (Z,Z)-farnesyl diphosphate]. By applying the method to crude protein extracts from various organs of Arabidopsis thaliana, Nicotiana attenuata, Populus trichocarpa, and Picea abies, we could determine their IDS activity in a reproducible fashion.

Organic complexed superphosphates (CSP): physicochemical characterization and agronomical properties

A new type of superphosphate (organic complexed superphosphate (CSP)) has been developed by the introduction of organic chelating agents, preferably a humic acid (HA), into the chemical reaction of single superphosphate (SSP) production. This modification yielded a product containing monocalcium phosphate complexed by the chelating organic agent through Ca bridges. Theoretically, the presence of these monocalcium-phosphate-humic complexes (MPHC) inhibits phosphate fixation in soil, thus increasing P fertilizer efficiency. This study investigateed the structural and functional features of CSP fertilizers produced employing diverse HA with different structural features. To this end were used complementary analytical techniques: solid-phase ³¹P NMR, ¹³C NMR, laser-confocal microscopy, X-ray diffraction, and molecular modeling. Finally, the agronomical efficiency of four CSP have been compared with that of SSP as P sources for wheat plants grown in both alkaline and acidic soils in greenhouse pot trials under controlled conditions. The results obtained from the diverse analytical studies showed the formation of MPHC in CSP. Plant-soil studies showed that CSP products were more efficient than SSP in providing available phosphate for wheat plants cultivated in various soils with different physicochemical features. This fact is probably associated with the ability of CSP complexes to inhibit phosphate fixation in soil.

Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II

Pyrophosphate ion (PP(i)) release after nucleotide incorporation is a necessary step for RNA polymerase II (pol II) to enter the next nucleotide addition cycle during transcription elongation. However, the role of pol II residues in PP(i) release and the mechanistic relationship between PP(i) release and the conformational change of the trigger loop remain unclear. In this study, we constructed a Markov state model (MSM) from extensive all-atom molecular dynamics (MD) simulations in the explicit solvent to simulate the PP(i) release process along the pol II secondary channel. Our results show that the trigger loop has significantly larger intrinsic motion after catalysis and formation of PP(i), which in turn aids PP(i) release mainly through the hydrogen bonding between the trigger loop residue H1085 and the (Mg-PP(i))(2-) group. Once PP(i) leaves the active site, it adopts a hopping model through several highly conserved positively charged residues such as K752 and K619 to release from the pol II pore region of the secondary channel. These positive hopping sites form favorable interactions with PP(i) and generate four kinetically metastable states as identified by our MSM. Furthermore, our single-mutant simulations suggest that H1085 and K752 aid PP(i) exit from the active site after catalysis, whereas K619 facilitates its passage through the secondary channel. Finally, we suggest that PP(i) release could help the opening motion of the trigger loop, even though PP(i) release precedes full opening of the trigger loop due to faster PP(i) dynamics. Our simulations provide predictions to guide future experimental tests.

Pyrophosphate coupling with chelant-enhanced soil flushing of field contaminated soils for heavy metal extraction

This study investigated the influence of flushing duration, [S,S]-ethylenediaminedisuccinic acid (EDDS) dosage, humic acid and various combinations of ethylenediaminetetraacetic acid (EDTA), EDDS and tetrasodium pyrophosphate (Na(4)P(2)O(7)) on metal extraction during soil flushing, through column experiments. A lesser extent of enhancement in metal extraction efficiencies was found when the flushing duration and the dosage of EDDS was doubled, compared to their efficiencies measured at pore volume 100. Metal extraction efficiency was mainly influenced by the initial metal distribution in the soils rather than the flushing duration and the EDDS-to-metal molar ratio. Humic acid of less than 10mg/L as dissolved organic carbon (DOC) posed an insignificant effect on metal extraction during EDDS enhanced soil flushing. The extraction rate of Ni by EDTA and EDDS was time dependent, and was initially fast in the case of EDDS, whereas it was slow for EDTA. However, the overall Ni extraction efficiency by EDTA was higher when the flushing time was longer. Na(4)P(2)O(7) promoted the mineral dissolution which enhanced the metal extraction as a result of soil disruption. The order of metal extraction by Na(4)P(2)O(7) was Ni>Cr>Cu, probably be due to the different affinities between metals and P(2)O(7)(4-).