Gypsum, crop rotation, and cover crop impacts on soil organic carbon and biological dynamics in rainfed transitional no-till corn-soybean systems.

Soil organic carbon (SOC), a core soil quality indicator, is influenced by management practices. The objective of our 2012-2016 study was to elucidate the impact of gypsum, crop rotation, and cover crop on SOC and several of its biological indicators under no-till in Alabama (Shorter), Indiana (Farmland), and Ohio (Hoytville and Piketon) in the USA. A randomized complete block design in factorial arrangement with gypsum (at 0, 1.1, and 2.2 Mg/ha annually), rye (Secale cereal L.) vs no cover crop, and rotation (continuous soybean [Glycine max (L) Merr., SS] vs corn [Zea mays, L.]-soybean, both the CS and SC phases) was conducted. Composite soils were collected (0-15 cm and 15-30 cm) in 2016 to analyze microbial biomass C (SMBC), SOC, total N, active C, cold and hot-water extractable C, C and N pool indices (CPI and NPI), and C management index (CMI). Results varied for main effects of gypsum, crop rotation, and cover crop on SOC pools, total N, and SOC lability within and across the sites. Gypsum at 2.2 Mg/ha increased SMBC within sites and by 41% averaged across sites. Likewise, gypsum increased SMBC:SOC, active C, and hot-water C (as indicators of labile SOC) averaged across sites. CS rotation increased SOC, active C, CPI, and CMI compared to SS, but decreased SMBC and SMBC:SOC within and across sites. CPI had a significant relationship with NPI across all sites (R2 = 0.90). Management sensitive SOC pools that responded to the combined gypsum (2.2 Mg/ha), crop rotation (CS), and cover crop (rye) were SMBC, SMBC:SOC, active C, and CMI via SMBC. These variables can provide an early indication of management-induced changes in SOC storage and its lability. Our results show that when SOC accumulates, its lability has decreased, presumably because the SMBC has processed all readily available C into a less labile form.

The structure of Synechococcus elongatus enolase reveals key aspects of phosphoenolpyruvate binding.

A structure-function characterization of Synechococcus elongatus enolase (SeEN) is presented, representing the first structural report on a cyanobacterial enolase. X-ray crystal structures of SeEN in its apoenzyme form and in complex with phosphoenolpyruvate are reported at 2.05 and 2.30 Šresolution, respectively. SeEN displays the typical fold of enolases, with a conformationally flexible loop that closes the active site upon substrate binding, assisted by two metal ions that stabilize the negatively charged groups. The enzyme exhibits a catalytic efficiency of 1.2 × 105 M-1 s-1 for the dehydration of 2-phospho-D-glycerate, which is comparable to the kinetic parameters of related enzymes. These results expand the understanding of the biophysical features of these enzymes, broadening the toolbox for metabolic engineering applications.

Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina.

Heme catalases remove hydrogen peroxide by catalyzing its dismutation into water and molecular oxygen, thereby protecting the cell from oxidative damage. The Atacama plateau in northern Argentina, located 4000 m above sea level, is a desert area characterized by extreme UV radiation, high salinity and a large temperature variation between day and night. Here, the heme catalase KatE1 from an Atacama Acinetobacter sp. isolate was cloned, expressed and purified, with the aim of investigating its extremophilic properties. Kinetic and stability assays indicate that KatE1 is maximally active at 50°C in alkaline media, with a nearly unchanged specific activity between 0°C and 40°C in the pH range 5.5-11.0. In addition, its three-dimensional crystallographic structure was solved, revealing minimal structural differences compared with its mesophilic and thermophilic analogues, except for a conserved methionine residue on the distal heme side, which is proposed to comprise a molecular adaptation to oxidative damage.

Visualizing the superfamily of metallo-ß-lactamases through sequence similarity network neighborhood connectivity analysis.

Protein sequence similarity networks (SSNs) constitute a convenient approach to analyze large polypeptide sequence datasets, and have been successfully applied to study a number of protein families over the past decade. SSN analysis is herein combined with traditional cladistic and phenetic phylogenetic analysis (respectively based on multiple sequence alignments and all-against-all three-dimensional protein structure comparisons) in order to assist the ancestral reconstruction and integrative revision of the superfamily of metallo-ß-lactamases (MBLs). It is shown that only 198 out of 15,292 representative nodes contain at least one experimentally obtained protein structure in the Protein Data Bank or a manually annotated SwissProt entry, that is to say, only 1.3 % of the superfamily has been functionally and/or structurally characterized. Besides, neighborhood connectivity coloring, which measures local network interconnectivity, is introduced for detection of protein families within SSN clusters. This approach provides a clear picture of how many families remain unexplored in the superfamily, while most MBL research is heavily biased towards a few families. Further research is suggested in order to determine the SSN topological properties, which will be instrumental for the improvement of automated sequence annotation methods.

Injury frequency and severity in crayfish communities as indicators of physical habitat quality and water quality within agricultural headwater streams.

Crayfishes (Decapoda) are common inhabitants of agricultural headwater streams in the Midwestern USA that have been impacted by physical habitat degradation and contamination by agricultural pollutants. The frequency and severity of injuries within crayfish communities are indicators of crayfish aggression, which is influenced by physical, chemical, and biotic factors. Previous studies have not evaluated the relationships of the frequency and severity of crayfish injuries with physical habitat quality, water quality, and biotic factors within agricultural headwater streams. Understanding these relationships will assist with determining if crayfish injury variables can serve as an indicator of physical habitat quality or water quality in these small degraded streams. We sampled crayfishes, documented the frequency and type of injuries, and measured instream habitat and water chemistry in 2014 and 2015 within 12 agricultural headwater streams in Indiana, Michigan, and Ohio. We documented five native crayfish species from 1641 adult captures. The most abundant species were Faxonius rusticus, Faxonius immunis, and Faxonius propinquus. Linear mixed effect model analyses indicated that four crayfish injury response variables were positively correlated (p < 0.05) with crayfish density, physical habitat quality, and water velocity diversity and that crayfish injury response variables were more strongly correlated with crayfish density than physical habitat quality or water quality. Our results indicate that response variables describing the severity and frequency of crayfish injuries can be effective indicators of physical habitat quality in agricultural headwater streams.

Long-term sorption of lincomycin to biochars: The intertwined roles of pore diffusion and dissolved organic carbon.

Sequestration of anthropogenic antibiotics by biochars from waters may be a promising strategy to minimize environmental and human health risks of antibiotic resistance. This study investigated the long-term sequestration of lincomycin by 17 slow-pyrolysis biochars using batch sorption experiments during 365 days. Sorption kinetics were well fitted to the Weber-Morris intraparticle diffusion model for all tested biochars with the intraparticle diffusion rate constant (kid) of 25.3-166 µg g-1 day-0.5 and intercept constant (Cid) of 39.0-339 µg g-1, suggesting that the sorption kinetics were controlled by fast initial sorption and slow pore diffusion. The quasi-equilibrium sorption isotherms became more nonlinear with increasing equilibration time at 1, 7, 30, and 365 days, likely due to increasing abundance of heterogeneous sorption sites in biochars over time. Intriguingly, low-temperature (300 °C) and high-temperature (600 °C) biochars had faster sorption kinetics than intermediate-temperature (400-500 °C) biochars at the long term, which was attributed to greater specific surface area and pore volume of high-temperature biochars and the substantial and continuous release of dissolved organic carbon (DOC) from low-temperature biochars, respectively. DOC release enhanced lincomycin sorption by decreasing biochar particle size and/or increasing the accessibility of sorption sites and pores initially blocked by DOC. Additionally, a large fraction (>75%) of sorbed lincomycin in biochars after a 240-day equilibration could not be extracted by the acetonitrile/methanol extractant. The strong sorption and low extraction recovery demonstrated the great potential of biochars as soil amendments for long-term sequestration of antibiotics in-situ.

Deciphering the number and location of active sites in the monomeric glyoxalase I of Zea mays.

Detoxification of methylglyoxal, a toxic by-product of central sugar metabolism, is a major issue for all forms of life. The glyoxalase pathway evolved to effectively convert methylglyoxal into d-lactate via a glutathione hemithioacetal intermediate. Recently, we have shown that the monomeric glyoxalase I from maize exhibits a symmetric fold with two cavities, potentially harboring two active sites, in analogy with homodimeric enzyme surrogates. Here we confirm that only one of the two cavities exhibits glyoxalase I activity and show that it adopts a tunnel-shaped structure upon substrate binding. Such conformational change gives rise to independent binding sites for glutathione and methylglyoxal in the same active site, with important implications for the molecular reaction mechanism, which has been a matter of debate for several decades. DATABASE: Structural data are available in The Protein Data Bank database under the accession numbers 6BNN, 6BNX, and 6BNZ.

Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase.

Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.

Investigation of Atrazine Sorption to Biochar With Titration Calorimetry and Flow-Through Analysis: Implications for Design of Pollution-Control Structures.

Atrazine is one of the most common broad-leaf herbicides used in the world. However, due to extensive use for many years, atrazine often appears in surface and groundwater. Atrazine transport is inhibited by degradation or sorption to soil components, especially organic matter. Biochar is a charcoal-like material produced from pyrolysis of biomass. Due to the amount and type of functional groups found on biochar, this product has shown potential for sorption of atrazine from solution. There is an interest in developing best management practices utilizing biochar to filter atrazine from non-point drainage with pollution-control structures such as blind inlets. The objective of this study was to explore the kinetics and thermodynamics of atrazine sorption to biochar using two different approaches: flow-through sorption cells and isothermal titration calorimetry (ITC). Twenty-five milligrams of an oak (Quercus spp.)-derived biochar was suspended in water and titrated 25 times (0.01 mL per titration) with atrazine at three different concentrations, and by a single titration (0.25 mL), with heat of reaction directly measured with ITC. A benchtop atrazine sorption study that simulated the titration experiment was also conducted. A continuous flow-through system was used to quantify the impact of contact time on atrazine sorption to biochar. Atrazine sorption to biochar displayed both exothermic and endothermic signals within each titration, although the net reaction was exothermic and proportional to the degree of sorption. Net enthalpy was -4,231 ± 130 kJ mole-1 atrazine sorbed. The existence of both exotherms and endotherms within a single titration, plus observation of an initial fast reaction phase from 0 to 300 s followed by a slower phase, suggested multiple sorption mechanisms to biochar. Results of flow-through tests supported kinetics observations, with the 300 s contact time removing much more atrazine compared to 45 s, while 600 s improved little compared to 300 s. Based on flow-through results, annual atrazine removal goal of 50%, and typical Midwestern U.S. tile drainage conditions, a pollution-control structure implementing this biochar sample would require 32 and 4 Mg for a design utilizing a contact time of 45 and 300 s, respectively. Future work is necessary for estimating degradation of atrazine sorbed to biochar.

Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift.

Malyl-CoA lyase (MCL) is an Mg2+-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Šresolution X-ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg2+ is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl-CoA lyase complexed with Mg2+, oxalate and CoA allows a detailed analysis of the domain motion of the enzyme caused by substrate binding. Alignment of the structures shows that a simple hinge motion centered on the conserved residues Phe268 and Thr269 moves the C-terminal domain by about 30° relative to the rest of the molecule. This domain motion positions a conserved aspartate residue located in the C-terminal domain in the active site of the adjacent monomer, which may serve as a general acid/base in the catalytic mechanism.

Antifungal pharmacodynamics: Latin America's perspective

Abstract The current increment of invasive fungal infections and the availability of new broad-spectrum antifungal agents has increased the use of these agents by non-expert practitioners, without an impact on mortality. To improve efficacy while minimizing prescription errors and to reduce the high monetary cost to the health systems, the principles of pharmacokinetics (PK) and pharmacodynamics (PD) are necessary. A systematic review of the PD of antifungals agents was performed aiming at the practicing physician without expertise in this field. The initial section of this review focuses on the general concepts of antimicrobial PD. In vitro studies, fungal susceptibility and antifungal serum concentrations are related with different doses and dosing schedules, determining the PD indices and the magnitude required to obtain a specific outcome. Herein the PD of the most used antifungal drug classes in Latin America (polyenes, azoles, and echinocandins) is discussed.

Antifungal pharmacodynamics: Latin America's perspective.

The current increment of invasive fungal infections and the availability of new broad-spectrum antifungal agents has increased the use of these agents by non-expert practitioners, without an impact on mortality. To improve efficacy while minimizing prescription errors and to reduce the high monetary cost to the health systems, the principles of pharmacokinetics (PK) and pharmacodynamics (PD) are necessary. A systematic review of the PD of antifungals agents was performed aiming at the practicing physician without expertise in this field. The initial section of this review focuses on the general concepts of antimicrobial PD. In vitro studies, fungal susceptibility and antifungal serum concentrations are related with different doses and dosing schedules, determining the PD indices and the magnitude required to obtain a specific outcome. Herein the PD of the most used antifungal drug classes in Latin America (polyenes, azoles, and echinocandins) is discussed.

Cross-class metallo-ß-lactamase inhibition by bisthiazolidines reveals multiple binding modes.

Metallo-ß-lactamases (MBLs) hydrolyze almost all ß-lactam antibiotics and are unaffected by clinically available ß-lactamase inhibitors (ßLIs). Active-site architecture divides MBLs into three classes (B1, B2, and B3), complicating development of ßLIs effective against all enzymes. Bisthiazolidines (BTZs) are carboxylate-containing, bicyclic compounds, considered as penicillin analogs with an additional free thiol. Here, we show both l- and d-BTZ enantiomers are micromolar competitive ßLIs of all MBL classes in vitro, with Kis of 6-15 µM or 36-84 µM for subclass B1 MBLs (IMP-1 and BcII, respectively), and 10-12 µM for the B3 enzyme L1. Against the B2 MBL Sfh-I, the l-BTZ enantiomers exhibit 100-fold lower Kis (0.26-0.36 µM) than d-BTZs (26-29 µM). Importantly, cell-based time-kill assays show BTZs restore ß-lactam susceptibility of Escherichia coli-producing MBLs (IMP-1, Sfh-1, BcII, and GOB-18) and, significantly, an extensively drug-resistant Stenotrophomonas maltophilia clinical isolate expressing L1. BTZs therefore inhibit the full range of MBLs and potentiate ß-lactam activity against producer pathogens. X-ray crystal structures reveal insights into diverse BTZ binding modes, varying with orientation of the carboxylate and thiol moieties. BTZs bind the di-zinc centers of B1 (IMP-1; BcII) and B3 (L1) MBLs via the free thiol, but orient differently depending upon stereochemistry. In contrast, the l-BTZ carboxylate dominates interactions with the monozinc B2 MBL Sfh-I, with the thiol uninvolved. d-BTZ complexes most closely resemble ß-lactam binding to B1 MBLs, but feature an unprecedented disruption of the D120-zinc interaction. Cross-class MBL inhibition therefore arises from the unexpected versatility of BTZ binding.

Sorption of Lincomycin by Manure-Derived Biochars from Water.

The presence of antibiotics in agroecosystems raises concerns about the proliferation of antibiotic-resistant bacteria and adverse effects to human health. Soil amendment with biochars pyrolized from manures may be a win-win strategy for novel manure management and antibiotics abatement. In this study, lincomycin sorption by manure-derived biochars was examined using batch sorption experiments. Lincomycin sorption was characterized by two-stage kinetics with fast sorption reaching quasi-equilibrium in the first 2 d, followed by slow sorption over 180 d. The fast sorption was primarily attributed to surface adsorption, whereas the long-term slow sorption was controlled by slow diffusion of lincomycin into biochar pore structures. Two-day sorption experiments were performed to explore effects of biochar particle size, solid/water ratio, solution pH, and ionic strength. Lincomycin sorption to biochars was greater at solution pH 6.0 to 7.5 below the dissociation constant of lincomycin (7.6) than at pH 9.9 to 10.4 above its dissociation constant. The enhanced lincomycin sorption at lower pH likely resulted from electrostatic attraction between the positively charged lincomycin and the negatively charged biochar surfaces. This was corroborated by the observation that lincomycin sorption decreased with increasing ionic strength at lower pH (6.7) but remained constant at higher pH (10). The long-term lincomycin sequestration by biochars was largely due to pore diffusion plausibly independent of solution pH and ionic composition. Therefore, manure-derived biochars had lasting lincomycin sequestration capacity, implying that biochar soil amendment could significantly affect the distribution, transport, and bioavailability of lincomycin in agroecosystems.

Polyphenol-Aluminum Complex Formation: Implications for Aluminum Tolerance in Plants.

Natural polyphenols may play an important role in aluminum detoxification in some plants. We examined the interaction between Al(3+) and the purified high molecular weight polyphenols pentagalloyl glucose (940 Da) and oenothein B (1568 Da), and the related compound methyl gallate (184 Da) at pH 4 and 6. We used spectrophotometric titration and chemometric modeling to determine stability constants and stoichiometries for the aluminum-phenol (AlL) complexes. The structures and spectral features of aluminum-methyl gallate complexes were evaluated with quantum chemical calculations. The high molecular weight polyphenols formed Al3L2 complexes with conditional stability constants (ß) ∼ 1 × 10(23) at pH 6 and AlL complexes with ß âˆ¼ 1 × 10(5) at pH 4. Methyl gallate formed AlL complexes with ß = 1 × 10(6) at pH 6 but did not complex aluminum at pH 4. At intermediate metal-to-polyphenol ratios, high molecular weight polyphenols formed insoluble Al complexes but methyl gallate complexes were soluble. The high molecular weight polyphenols have high affinities and solubility features that are favorable for a role in aluminum detoxification in the environment.

Demonstration of Therapeutic Equivalence of Fluconazole Generic Products in the Neutropenic Mouse Model of Disseminated Candidiasis.

Some generics of antibacterials fail therapeutic equivalence despite being pharmaceutical equivalents of their innovators, but data are scarce with antifungals. We used the neutropenic mice model of disseminated candidiasis to challenge the therapeutic equivalence of three generic products of fluconazole compared with the innovator in terms of concentration of the active pharmaceutical ingredient, analytical chemistry (liquid chromatography/mass spectrometry), in vitro susceptibility testing, single-dose serum pharmacokinetics in infected mice, and in vivo pharmacodynamics. Neutropenic, five week-old, murine pathogen free male mice of the strain Udea:ICR(CD-2) were injected in the tail vein with Candida albicans GRP-0144 (MIC = 0.25 mg/L) or Candida albicans CIB-19177 (MIC = 4 mg/L). Subcutaneous therapy with fluconazole (generics or innovator) and sterile saline (untreated controls) started 2 h after infection and ended 24 h later, with doses ranging from no effect to maximal effect (1 to 128 mg/kg per day) divided every 3 or 6 hours. The Hill's model was fitted to the data by nonlinear regression, and results from each group compared by curve fitting analysis. All products were identical in terms of concentration, chromatographic and spectrographic profiles, MICs, mouse pharmacokinetics, and in vivo pharmacodynamic parameters. In conclusion, the generic products studied were pharmaceutically and therapeutically equivalent to the innovator of fluconazole.

Structure of the novel monomeric glyoxalase I from Zea mays.

The glyoxalase system is ubiquitous among all forms of life owing to its central role in relieving the cell from the accumulation of methylglyoxal, a toxic metabolic byproduct. In higher plants, this system is upregulated under diverse metabolic stress conditions, such as in the defence response to infection by pathogenic microorganisms. Despite their proven fundamental role in metabolic stresses, plant glyoxalases have been poorly studied. In this work, glyoxalase I from Zea mays has been characterized both biochemically and structurally, thus reporting the first atomic model of a glyoxalase I available from plants. The results indicate that this enzyme comprises a single polypeptide with two structurally similar domains, giving rise to two lateral concavities, one of which harbours a functional nickel(II)-binding active site. The putative function of the remaining cryptic active site remains to be determined.

Structural analysis of ibuprofen binding to human adipocyte fatty-acid binding protein (FABP4).

Inhibition of human adipocyte fatty-acid binding protein (FABP4) has been proposed as a treatment for type 2 diabetes, fatty liver disease and atherosclerosis. However, FABP4 displays a naturally low selectivity towards hydrophobic ligands, leading to the possibility of side effects arising from cross-inhibition of other FABP isoforms. In a search for structural determinants of ligand-binding selectivity, the binding of FABP4 towards a group of small molecules structurally related to the nonsteroidal anti-inflammatory drug ibuprofen was analyzed through X-ray crystallography. Several specific hydrophobic interactions are shown to enhance the binding affinities of these compounds, whereas an aromatic edge-to-face interaction is proposed to determine the conformation of bound ligands, highlighting the importance of aromatic interactions in hydrophobic environments.

An optimized mouse thigh infection model for enterococci and its impact on antimicrobial pharmacodynamics.

Negligible in vivo growth of enterococci and high-level dispersion of data have led to inaccurate estimations of antibiotic pharmacodynamics (PD). Here we improved an in vivo model apt for PD studies by optimizing the in vitro culture conditions for enterococci. The PD of vancomycin (VAN), ampicillin-sulbactam (SAM), and piperacillin-tazobactam (TZP) against enterococci were determined in vivo, comparing the following different conditions of inoculum preparation: aerobiosis, aerobiosis plus mucin, and anaerobiosis plus mucin. Drug exposure was expressed as the ratio of the area under the concentration-time curve for the free, unbound fraction of the drug to the MIC (fAUC/MIC) (VAN) or the time in a 24-h period that the drug concentration for the free, unbound fraction exceeded the MIC under steady-state pharmacokinetic conditions (fT(>MIC)) (SAM and TZP) and linked to the change in log10 CFU/thigh. Only anaerobiosis plus mucin enhanced the in vivo growth, yielding significant PD parameters with all antibiotics. In conclusion, robust in vivo growth of enterococci was crucial for better determining the PD of tested antibacterial agents, and this was achieved by optimizing the procedure for preparing the inoculum.

A novel member of glycoside hydrolase family 30 subfamily 8 with altered substrate specificity.

Endoxylanases classified into glycoside hydrolase family 30 subfamily 8 (GH30-8) are known to hydrolyze the hemicellulosic polysaccharide glucuronoxylan (GX) but not arabinoxylan or neutral xylooligosaccharides. This is owing to the specificity of these enzymes for the α-1,2-linked glucuronate (GA) appendage of GX. Limit hydrolysis of this substrate produces a series of aldouronates each containing a single GA substituted on the xylose penultimate to the reducing terminus. In this work, the structural and biochemical characterization of xylanase 30A from Clostridium papyrosolvens (CpXyn30A) is presented. This xylanase possesses a high degree of amino-acid identity to the canonical GH30-8 enzymes, but lacks the hallmark ß8-α8 loop region which in part defines the function of this GH30 subfamily and its role in GA recognition. CpXyn30A is shown to have a similarly low activity on all xylan substrates, while hydrolysis of xylohexaose revealed a competing transglycosylation reaction. These findings are directly compared with the model GH30-8 enzyme from Bacillus subtilis, XynC. Despite its high sequence identity to the GH30-8 enzymes, CpXyn30A does not have any apparent specificity for the GA appendage. These findings confirm that the typically conserved ß8-α8 loop region of these enzymes influences xylan substrate specificity but not necessarily ß-1,4-xylanase function.