Unraveling Mg2+-RNA binding with atomistic molecular dynamics.

Interaction with divalent cations is of paramount importance for RNA structural stability and function. We report here a detailed molecular dynamics study of all the possible binding sites for Mg2+ on an RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics, which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases. Based on this, we simulate a carefully chosen set of models that allows us to quantify the effects of competition with monovalent cations, RNA flexibility, and RNA hybridization. Our simulations reproduce the decrease and increase of Mg2+ affinity due to ion competition and hybridization, respectively, and predict that RNA flexibility has a site-dependent effect. This suggests a nontrivial interplay between RNA conformational entropy and divalent cation binding.

Nonlinear biotic ligand model for assessing alleviation effects of Ca, Mg, and K on Cd toxicity to soybean roots.

Developing a nonlinear biotic ligand model (BLM) that considers the geometrical constraints for binding of different cations on biotic ligands will provide more reliable details about the hypothetical mechanism governing the alleviation of cadmium (Cd) toxicity by coexistent cations. Soybean seedlings under Cd stress produced by various activities of coexistent cations such as calcium (Ca2+), magnesium (Mg2+), and potassium (K+) were hydroponically assayed for Cd toxicity to soybean roots. The Cd2+ activity resulting in 50% reduction of root elongation (RE), EA 50, was used for assessing the Cd toxicity to the soybean seedling. Increasing Ca2+, Mg2+, and K+ activities resulted in a significant alleviation of Cd toxicity to soybean roots. This alleviation was markedly higher with increasing Ca2+ and K+ levels than with increasing Mg2+ level. In addition, EA 50 increased in nonlinear positive relationships with Ca2+ and Mg2+. The real data obtained from the soybean assay were thus used to develop the nonlinear BLM for Cd rhizotoxicity. Two parameters, competition equivalent and stability constant, indicated the profiles of the geometrical constraint and affinity of Ca2+, Mg2+, and K+ binding on the soybean root surface to alleviate Cd toxicity. Compared with the traditional linear BLM, the nonlinear BLM provided more precise predictions of relative root elongation (RRE) and EA 50. Therefore, adopting the nonlinear BLM approach will successfully improve the monitoring and assessment of heavy metal toxicity to terrestrial plants.

Magnetite alleviating calcification of anaerobic granular sludge (AnGS): Electron transfer enhancement and ion competition.

Calcification accompanied by deactivation of anaerobic granular sludge (AnGS) is a continuing challenge for high calcium wastewater treatment. The interaction between Ca2+ and extracellular polymeric substances (EPS) is a precondition for this problem. In this study, magnetite for activity recovery and calcification alleviation simultaneously of AnGS under high calcium stress was investigated. The results showed that, in the presence of magnetite, the relative biogas production increased by 13.2 % with the higher activities of key enzymes involved in methanogenesis. Methanosarcina turned into the dominant methanogens, and syntrophic bacteria such as Chloroflexi, Synergistota were enriched, which indicated the enhancement of electron transfer by magnetite, supported by an 18 % increase of the electron transfer system (ETS) activity. Further characterizations of AnGS suggested that the granule calcification was alleviated with a final decrease of 13-40 % calcium content of AnGS with particle size of 1-2.5 mm. Besides, calcium was partially substituted by iron in the EPS, and the secretion of EPS especially proteins decreased. Batch tests demonstrated the competition between Fe2+ dissolved from magnetite and Ca2+, which interfered the interaction between Ca2+ and EPS, so the granule calcification was prevented. Therefore, magnetite played a pluripotent role in the alleviation of granule calcification and deactivation in situ via (1) enhancing electron transfer, and (2) blocking the complex between Ca2+ and EPS. This study provides a novel insight into the application of conductive metal materials in biological wastewater treatment systems suffering from high calcium attack.

The behavior of arsenic accumulation in onion (Allium cepa) structures by irrigation water: effect of phosphates and arsenic on the total bioactive compounds and antioxidant capacity.

The presence of arsenic (As) in irrigation water is a threat to agricultural crops as well as human health. The presence of arsenic and phosphorous in irrigation water influences the behavior of bioaccumulation, biotransfer, and total bioactive compounds in the distinct parts of the onion structure. The present work evaluates the behavior of the bioaccumulation and biotransfer of As in the structures of onion (Allium cepa) through a composite central design and response surface method. The factors employed include the concentration of arsenic (V) and phosphate (V) in the nutritive solution. Additionally, this study analyzes the behavior of the effect that the induced stress has on the total bioactive compounds (phenols and flavonoids) and antioxidant capacity (ABTS and DPPH) in the onion roots. The results showed that the physiological properties, bioaccumulation factors, As transference, and the total bioactive compounds in the onion structure are affected by the competition of As and phosphates (P(V)) in the irrigation water. For concentrations of As and phosphorous of 450 µg L-1 and 0.30 mg L-1 respectively in irrigation water, there are negative effects on the equatorial diameter of the bulb (DE), length, weight of the leaf, and weight of the bulb. Besides, the transference and bioaccumulation factors range from 0.02 to 0.22 and from 2.15 to 7.81, respectively, suggesting that the plant has the ability to accumulate As but exhibits a low translocation ability of As from the root to aerial organs. Besides, it is found for central concentrations of As and phosphorous (450 µg L-1 and 0.30 mg L-1, respectively) in irrigation water, a greater production occurs in total phenolic compounds and antioxidant capacity (ABTS and DPPH) as a response to the stress generated by As.

Cation valence dependence of hydrogen bond and stacking potentials in DNA mesoscopic models.

Monovalent and divalent cations play a crucial role in living cells and for molecular techniques such as PCR. Here we evaluate DNA melting temperatures in magnesium (Mg2+) and magnesium­potassium (Mg2++ K+) buffers with a mesoscopic model that allows us to estimate hydrogen bonds and stacking interaction potentials. The Mg2+ and Mg2++ K+ results are compared to previous calculations for sodium ions (Na+), in terms of equivalent sodium concentration and ionic strength. Morse potentials, related to hydrogen bonding, were found to be essentially constant and unaffected by cation conditions. However, for stacking interactions we find a clear dependence with ionic strength and cation valence. The highest ionic strength variations, for both hydrogen bonds and stacking interactions, was found at the sequence terminals. This suggests that end-to-end interactions in DNA will be strongly dependent on cation valence and ionic strength.

Minimizing ion competition boosts volatile metabolome coverage by secondary electrospray ionization orbitrap mass spectrometry.

Secondary electrospray ionization high-resolution mass spectrometry (SESI-HRMS) is an emerging technique for the detection of volatile metabolites. However, sensitivity and reproducibility of SESI-HRMS have limited its applications in untargeted metabolomics profiling. Ion suppression in the SESI source has been considered to be the main cause. Here, we show that besides ion suppression, ion competition in the C-trap of Orbitrap instruments is another important factor that influences sensitivity and reproducibility of SESI-MS. Instead of acquiring the full mass-to-charge ratio (m/z) range, acquisition of consecutive m/z windows to minimize the ion competition effect allows the detection of more features. m/z window ranges are optimized to fill the C-trap either with an equal number of features or an equal cumulative intensity per window. Considering a balance between maximizing scanning speed and minimizing ion competition, splitting the m/z = 50-500 range into 4 windows is selected for measuring human breath and bacterial culture samples on SESI-Orbitrap MS, corresponding to a duty cycle of 2.3 s at a resolution of 140'000. In a small cohort of human subjects, the proposed splitting into 4 windows allows three times more features to be detected compared to the classical full m/z range method.

Evaluation of component additive modelling approach for europium adsorption on 2:1 clays: Experimental, thermodynamic databases, and models.

This study evaluates the component additive approach for Eu adsorption on mixtures of smectite and illite, which are the most common clays used as barriers for contaminant retention in waste repositories. A thorough set of Eu adsorption data for Na-exchanged smectite and illite that encompasses a wide range of pH values, ionic strengths, and Eu concentrations was provided. This database is likely one of the largest sorption databases available for Eu in 2:1 clays, making it appropriate for sorption model calibration. The main adsorption mechanisms considered were surface complexation, on weak and strong clay edge sites, and cation exchange. Further, the role of principal ions, which are naturally leached from clays, as competitive factors for Eu retention, was evaluated in the modelling calculations. The main uncertainties related to the modelling procedures and the use of different thermodynamic data on sorption modelling were outlined. The reactions and parameters successful in modelling Eu adsorption on individual clays were used without any modification to model Eu adsorption on illite/smectite mixtures, wherein only the relative mineral proportions were considered. The fit of the sorption data in the mixed clay system was satisfactory, indicating that, in 2:1 clays, Eu sorption is an additive process, which stresses the predictive capacity of the component additive approach in these systems. This is an important support for assessing the performance of barrier materials for contaminant migration under different geochemical conditions.

Nutrient release and ammonium sorption by poultry litter and wood biochars in stormwater treatment.

The feasibility of using biochar as a filter medium in stormwater treatment facilities was evaluated with a focus on ammonium retention. Successive batch extractions and batch ammonium sorption experiments were conducted in both deionized (DI) water and artificial stormwater using poultry litter (PL) and hardwood (HW) biochars pyrolyzed at 400°C and 500°C. No measureable nitrogen leached from HW biochars except 0.07 µmol/g of org-N from 400°C HW biochar. PL biochar pyrolyzed at 400°C leached 120-127 µmol/g of nitrogen but only 7.1-8.6 µmol/g of nitrogen when pyrolyzed at 500°C. Ammonium sorption was significant for all biochars. At a typical ammonium concentration of 2mg/L in stormwater, the maximum sorption was 150 mg/kg for PL biochar pryolyzed at 400°C. In stormwater, ion competition (e.g. Ca(2+)) suppressed ammonium sorption compared to DI water. Surprisingly, ammonium sorption was negatively correlated to the BET surface area of the tested biochars, but increased linearly with cation exchange capacity. Cation exchange capacity was the primary mechanism controlling ammonium sorption and was enhanced by pyrolysis at 400°C, while BET surface area was enhanced by pyrolysis at 500°C. The optimal properties (BET surface area, CEC, etc.) of biochar as a sorbent are not fixed but depend on the target pollutant. Stormwater infiltration column experiments in sand with 10% biochar removed over 90% of ammonium with influent ammonium concentration of 2mg/L, compared to only 1.7% removal in a sand-only column, indicating that kinetic limitations on sorption were minor for the storm conditions studied. Hardwood and poultry litter biochar pyrolyzed at 500°C and presumably higher temperature may be viable filter media for stormwater treatment facilities, as they showed limited release of organic and inorganic nutrients and acceptable ammonium sorption.

Analyzing LC-MS/MS data by spectral count and ion abundance: two case studies.

In comparative proteomics studies, LC-MS/MS data is generally quantified using one or both of two measures: the spectral count, derived from the identification of MS/MS spectra, or some measure of ion abundance derived from the LC-MS data. Here we contrast the performance of these measures and show that ion abundance is the more sensitive. We also examine how the conclusions of a comparative analysis are influenced by the manner in which the LC-MS/MS data is 'rolled up' to the protein level, and show that divergent conclusions obtained using different rollups can be informative. Our analysis is based on two publicly available reference data sets, BIATECH-54 and CPTAC, which were developed for the purpose of assessing methods used in label-free differential proteomic studies. We find that the use of the ion abundance measure reveals properties of both data sets not readily apparent using the spectral count.