Membrane intercalation-enhanced photodynamic inactivation of bacteria by a metallacycle and TAT-decorated virus coat protein.

Antibiotic resistance has become one of the major threats to global health. Photodynamic inactivation (PDI) develops little antibiotic resistance; thus, it becomes a promising strategy in the control of bacterial infection. During a PDI process, light-induced reactive oxygen species (ROS) damage the membrane components, leading to the membrane rupture and bacteria death. Due to the short half-life and reaction radius of ROS, achieving the cell-membrane intercalation of photosensitizers is a key challenge for PDI of bacteria. In this work, a tetraphenylethylene-based discrete organoplatinum(II) metallacycle (1) acts as a photosensitizer with aggregation-induced emission. It self-assembles with a transacting activator of transduction (TAT) peptide-decorated virus coat protein (2) through electrostatic interactions. This assembly (3) exhibits both ROS generation and strong membrane-intercalating ability, resulting in significantly enhanced PDI efficiency against bacteria. By intercalating in the bacterial cell membrane or entering the bacteria, assembly 3 decreases the survival rate of gram-negative Escherichia coli to nearly zero and that of gram-positive Staphylococcus aureus to ∼30% upon light irradiation. This study has wide implications from the generation of multifunctional nanomaterials to the control of bacterial infection, especially for gram-negative bacteria.

Kinetics and mechanistic study on degradation of prednisone acetate by ozone.

Prednisone acetate (PNSA) is one of the regular glucocorticoid medicines that have been detected in surface water. In this work, the removal of PNSA by ozone was systematically studied under various conditions, and degradation intermediates and reaction pathways were proposed. The results showed that aqueous ozonation was able to remove PNSA effectively, and low pH favored this reaction. The addition of tertiary butanol did not inhibit the oxidation of PNSA by ozone, suggesting that the degradation was caused mainly by the direct oxidation effect of ozone molecules. Moreover, the presence of carboxylated or hydroxylated multiwalled carbon nanotubes can enhance the removal efficiency of PNSA by ozone. Under neutral and acidic conditions, the degradation of PNSA followed pseudo-first-order reaction. Seven intermediates were detected via liquid chromatography-mass spectrometry, and the degradation pathways were then proposed by considering the relative charge density of the frontier orbitals calculated with the Gaussian program. The electrophilic reaction and the Criegee mechanism were the primary reaction mechanisms in the degradation of PNSA by ozone. Formic acid, acetic acid, and oxalic acid were detected as the final reaction products via ion chromatography. Additionally, the aquatic toxicity of the ozonation products was predicted using ECOSAR method. The biodegradation potentials of the pollutant and the ozonation products were estimated using BIOWINTM, suggesting that O3 treatment could significantly enhance the biodegradable potentials of PNSA and its transformation intermediates in the biological post-treatment process. This work can provide useful information for the treatment of PNSA-containing wastewaters.

Recent Advances in Applications of Acidophilic Fungi to Produce Chemicals.

Processing of fossil fuels is the major environmental issue today. Biomass utilization for the production of chemicals presents an alternative to simple energy generation by burning. Lignocellulosic biomass (cellulose, hemicellulose and lignin) is abundant and has been used for variety of purposes. Among them, lignin polymer having phenyl-propanoid subunits linked together either through C-C bonds or ether linkages can produce chemicals. It can be depolymerized by fungi using their enzyme machinery (laccases and peroxidases). Both acetic acid and formic acid production by certain fungi contribute significantly to lignin depolymerization. Fungal natural organic acids production is thought to have many key roles in nature depending upon the type of fungi producing them. Biological conversion of lignocellulosic biomass is beneficial over physiochemical processes. Laccases, copper containing proteins oxidize a broad spectrum of inorganic as well as organic compounds but most specifically phenolic compounds by radical catalyzed mechanism. Similarly, lignin peroxidases (LiP), heme containing proteins perform a vital part in oxidizing a wide variety of aromatic compounds with H2O2. Lignin depolymerization yields value-added compounds, the important ones are aromatics and phenols as well as certain polymers like polyurethane and carbon fibers. Thus, this review will provide a concept that biological modifications of lignin using acidophilic fungi can generate certain value added and environmentally friendly chemicals.

Organic acid pretreatment of oil palm trunk: effect on enzymatic saccharification and ethanol production.

Effective lignocellulosic biomass saccharification is one of the crucial requirements of biofuel production via fermentation process. Organic acid pretreatments have been gained much interests as one of the high potential methods for promoting enzymatic saccharification of lignocellulosic materials due to their lower hazardous properties and lower production of inhibitory by-products of fermentation than typical chemical pretreatment methods. In this study, three organic acids, including acetic acid, oxalic acid, and citric acid, were examined for improvement of enzymatic saccharification and bioethanol production from oil palm trunk biomass. Based on response surface methodology, oxalic acid pretreated biomass released the maximum reducing sugar of 144 mg/g-pretreated biomass at the optimum condition, which was higher than untreated samples for 2.30 times. The released sugar yield of oil palm trunk also corresponded to the results of FT-IR analysis, which revealed the physical modification of cellulose and hemicellulose surface structures of pretreated biomass. Nevertheless, citric acid pretreatment is the most efficient pretreatment method to improve bioethanol fermentation of Saccharomyces cerevisiae TISTR 5606 at 1.94 times higher than untreated biomass. These results highlighted the selection of organic acid pretreatment as a potential method for biofuel production from oil palm trunk feedstocks.

Flavor Compounds in Pixian Broad-Bean Paste: Non-Volatile Organic Acids and Amino Acids.

Non-volatile organic acids and amino acids are important flavor compounds in Pixian broad-bean paste, which is a traditional Chinese seasoning product. In this study, non-volatile organic acids, formed in the broad-bean paste due to the metabolism of large molecular compounds, are qualitatively and quantitatively determined by high-performance liquid chromatography (HPLC). Amino acids, mainly produced by hydrolysis of soybean proteins, were determined by the amino acid automatic analyzer. Results indicated that seven common organic acids and eighteen common amino acids were found in six Pixian broad-bean paste samples. The content of citric acid was found to be the highest in each sample, between 4.1 mg/g to 6.3 mg/g, and malic acid were between 2.1 mg/g to 3.6 mg/g ranked as the second. Moreover, fumaric acid was first detected in fermented bean pastes albeit with a low content. For amino acids, savory with lower sour taste including glutamine (Gln), glutamic acid (Glu), aspartic acid (Asp) and asparagines (Asn) were the most abundant, noted to be 6.5 mg/g, 4.0 mg/g, 6.4 mg/g, 4.9 mg/g, 6.2 mg/g and 10.2 mg/g, and bitter taste amino acids followed. More importantly, as important flavor materials in Pixian broad-bean paste, these two groups of substances are expected to be used to evaluate and represent the flavor quality of Pixian broad-bean paste. Moreover, the results revealed that citric acid, glutamic acid, methionine and proline were the most important flavor compounds. These findings are agreat contribution for evaluating the quality and further assessment of Pixian broad-bean paste.

Synthesis of Cyclic and Acyclic Pyrimidine Nucleosides Analogues with Anticipated Antiviral Activity.

A convenient method for preparation of cyclic and acyclic nucleosides was achieved by alkylation of 6-(2,4-dichlorophenoxymethyl) pyrimidine-2,4-dione (1) with a variety of acyclic and cyclic activated sugar analogues, namely (2-acetoxyethoxy)methyl acetate (3), 2-(acetoxymethoxy)propane-1,3-diyl dibenzoate (4), benzyloxymethyl acetate (5), 2-acetoxy-5-(benzoyloxymethyl)tetrahydrofuran-3,4-diyl dibenzoate (12), 5-chloro-2-((4-chlorobenzoyloxy)methyl) tetrahydrofuran-3-yl 4-chlorobenzoate (13) and 2-(acetoxymethyl)-6-bromotetrahydro-2H-pyran-3,4,5-triyl triacetate (14), respectively. Deprotection of the synthesized nucleosides was achieved by using methanolic ammonia. The structures of the newly synthesized nucleoside analogues were fully characterized by analytical methods (mass spectrometry, 1H NMR, 13C NMR, and elemental analysis).

Liposomal Circular Dichroism (L-CD) of Arenoyl Derivatives of Sphingolipids. Amplification of Cotton Effects in Ordered Lipid Bilayers.

Liposomal circular dichroism (L-CD) of acyclic amino alcohols exhibit amplification of Cotton effects when measured in highly uniform, unilamellar liposomes. The effect is likely due to intermolecular associations-H-aggregates-that self-assemble spontaneously within the lipid bilayer, and persists over long time scales. L-CD spectra of N,O,O'-tri-(6'methoxy-2'-naphthoyl)-d-erythro-sphingosine, or the corresponding dihydro-derivative (sphinganine), shows ~10-fold amplification of magnitudes of Cotton effects over conventional CD spectra recorded in isotropic solution.

Calibration-free quantitation in microchip zone electrophoresis with conductivity detection.

The relationship between electrophoretic mobility and molar conductivity has previously led to speculation on achieving quantitation in zone electrophoresis without calibration curves when using conductivity detection. However, little work in this area has been pursued, possibly because of the breakdown of simple sensitivity-mobility relationships when working with partially protonated species. This topic is revisited with the aid of electrophoretic simulation software that produces facile predictions of analyte sensitivity relative to an internal standard. Calibration curve slopes for over 50 analyte/internal standard/BGE combinations were measured with both unbiased and electrokinetically biased injections using microchip electrophoresis with conductivity detection. The results were compared to theoretical expectations as computed with PeakMaster software. Good agreement was observed, with some systems being predicted with quantitative accuracy while others showed significant deviations. Some mechanisms that can lead to deviations from theory are demonstrated, but the causes for some discrepancies are still not understood. Overall, this work exhibits another useful application for simulation software, particularly for disposable devices where device-specific calibration curves cannot be collected. It also serves as quantitative validation for some outputs of PeakMaster simulation software.

Determination of metabolic organic acids in cerebrospinal fluid by microchip electrophoresis.

A new MCE method for the determination of oxalic, citric, glycolic, lactic, and 2- and 3-hydroxybutyric acids, indicators of some metabolic and neurological diseases, in cerebrospinal fluid (CSF) was developed. MCE separations were performed on a PMMA microchip with coupled channels at lower pH (5.5) to prevent proteins interference. A double charged counter-ion, BIS-TRIS propane, was very effective in resolving the studied organic acids. The limits of detection (S/N = 3) ranging from 0.1 to 1.6 µM were obtained with the aid of contact conductivity detector implemented directly on the microchip. RSDs for migration time and peak area of organic acids in artificial and CSF samples were <0.8 and <9.7%, respectively. Recoveries of organic acids in untreated CSF samples on the microchip varied from 91 to 104%. Elimination of chloride interference, a major anionic constituent of CSF, has been reached by two approaches: (i) the use of coupled channels microchip in a column switching mode when approximately 97-99% of chloride was removed electrophoretically in the first separation channel and (ii) the implementation of micro-SPE with silver-form resin prior to the MCE analysis, which selectively removed chloride from undeproteinized CSF samples.

Theoretical and kinetic study of the hydrogen atom abstraction reactions of esters with H(O.)2 radicals.

This work details an ab initio and chemical kinetic study of the hydrogen atom abstraction reactions by the hydroperoxyl radical (HÈ®2) on the following esters: methyl ethanoate, methyl propanoate, methyl butanoate, methyl pentanoate, methyl isobutyrate, ethyl ethanoate, propyl ethanoate, and isopropyl ethanoate. Geometry optimizations and frequency calculations of all of the species involved, as well as the hindrance potential descriptions for reactants and transition states, have been performed with the Møller-Plesset (MP2) method using the 6-311G(d,p) basis set. A validation of all of the connections between transition states and local minima was performed by intrinsic reaction coordinate calculations. Electronic energies for all of the species are reported at the CCSD(T)/cc-pVTZ level of theory in kcal mol(-1) with the zero-point energy corrections. The CCSD(T)/CBS (extrapolated from CCSD(T)/cc-pVXZ, in which X = D, T, Q) was used for the reactions of methyl ethanoate + HÈ®2 radicals as a benchmark in the electronic energy calculations. High-pressure limit rate constants, in the temperature range 500-2000 K, have been calculated for all of the reaction channels using conventional transition state theory with asymmetric Eckart tunneling corrections. The 1-D hindered rotor approximation has been used for the low frequency torsional modes in both reactants and transition states. The calculated individual and total rate constants are reported for all of the reaction channels in each reaction system. A branching ratio analysis for each reaction site has also been investigated for all of the esters studied in this work.

Effect of low-molecular-weight organic acids on kinetics release and fractionation of phosphorus in some calcareous soils of western Iran.

Organic acid has been related to nutrient mobilization, mainly in phosphorus (P) insoluble utilization, and therefore enhances P bioavailability. In this study, we examined the effect of low-molecular-weight organic acids (malic, citric, and oxalic acids) on P release of some calcareous soils from western Iran. Fractionation and speciation of P in the soil solution were studied at the initial and final P release. Significantly different quantities of P were extracted by the organic acids. On average the maximum (1,554.9 mg kg(-1)) and the minimum (1,260.5 mg kg(-1)) P were extracted by 10 mM oxalic and malic acid, respectively. Power equation described well P release. In the initial stage of P release, the solution samples in soils were supersaturated with respect to hydroxyapatite and ß-TCP. At the end of P release, all solutions were undersaturated with phosphate minerals. The percentage of Fe-Al oxide fraction generally increased after P release, while carbonate and residual P fractions were decreased in all organic acids. Compared with the native soils, adding malic and citric acids had no effect on Fe-Al oxide fraction, but oxalic acid significantly reduced this fraction.

Enantioseparation of α-hydroxy acids by chiral ligand exchange CE with a dual central metal ion system.

Using two kinds of central metal ions in a background electrolyte, ligand exchange CE was investigated for the simultaneous enantioseparation of dl-malic, dl-tartaric, and dl-isocitric acids. Ligand exchange CE with 100 mM d-quinic acid as a chiral selector ligand and 10 mM Cu(II) ion as a central metal ion could enantioseparate dl-tartaric acid but not dl-malic acid or dl-isocitric acid. A dual central metal ion system containing 0.5 mM Al(III) ion in addition to 10 mM Cu(II) ion in the background electrolyte enabled the simultaneous enantioseparation of the three α-hydroxy acids. These results suggest that the use of a dual central metal ion system can be useful for enantioseparation by ligand exchange CE.

Quantifying instantaneous regeneration rates of plant leaf waxes using stable hydrogen isotope labeling.

Leaf waxes protect terrestrial plants from biotic and abiotic stresses and are important sedimentary biomarkers for terrestrial plants. Thus, understanding the production and ablation of leaf waxes is critical in plant physiology and for geochemical studies. However, there have been no accurate approaches to quantify leaf wax production at different time scales. In this study, we demonstrate a novel approach to study leaf wax regeneration by irrigating plants with a pulse of deuterium-enriched water, followed by measurements of leaf wax D/H ratios by gas chromatography/isotope-ratio mass spectrometry (GC/IRMS). We demonstrate the efficacy of this approach using the grass species Phleum pratense in a greenhouse environment. Using a binary isotope mass balance model, we are able to quantify the regeneration rates of the C(16), C(18) acids and leaf waxes (C(23)-C(31) n-alkanes; C(22)-C(30) n-acids) over a diurnal cycle. Our results show that within one day 33-47% of C(16) and C(18) acids are regenerated, and thus the recycling time for these compounds is 2-3 days. For C(22)-C(26) n-alkyl lipids, 7-21% are regenerated within one day and thus they require 5-16 days to recycle. In comparison, the recycling time for long-chain n-alkyl lipids (C(27)-C(31)) is as long as 71-128 days. Our approach can be applied to different plants at shorter or longer time scales by adjusting the degree of isotopic labeling, sampling intervals and the amount of irrigation water.

The synthesis and application of polyamino polycarboxylic bifunctional chelating agents.

Bifunctional chelating agents (BFCAs) are molecules which contain two different moieties: a strong metal chelating unit and a reactive functional group. The latter is directed to react with amines, thiols, alcohols or other reactive molecules to form stable covalent bonds while the chelating moiety is able to strongly coordinate a metal ion. In this way, it is possible to label a molecule of interest (e.g. an antibody or a peptide) with a metal or a radioactive metal ion. Of all the ligands reported so far, those based on a polyamino polycarboxylic structure are most efficient and are widely employed for the chelation of metal ions. The resulting metal complexes have found a broad range of applications in chemistry, biology and medicine. Diagnostic imaging (MRI, SPECT, PET), molecular imaging, tumour therapy and luminescent materials are only a few examples. The present critical review gives an overview of the syntheses and most important applications of polyamino polycarboxylic BFCAs (334 references).

Influence of organic acids on rheological and bread-making characteristics of fortified wheat flour.

Flour was fortified with premix containing ferrous fumarate and folic acid. Organic acids such as citric acid, malic acid and tartaric acid, which are promoters of iron bioavailability, were added at three levels and their influence on rheological and bread-making characteristics was studied. Farinograph water absorption increased with fortificants, but with addition of organic acids there was a decrease. Maximum pressure was 77 mm in control, which increased to 78-88 mm with the addition of different acids to the fortified flour. Addition of organic acids to fortified flour brought about a decrease in peak viscosity, hot paste viscosity, cold paste viscosity and setback values. The L, a and b values of fortified breads were similar to that of control. Sensory analysis revealed marginal differences in the overall quality of breads prepared with fortified flour with the addition of organic acids.

Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids.

All-atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic beta-amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using beta(3)-homo-Alanine (beta(3)-hAla) diamide in water with SCC-DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the beta(3)-hAla diamide in water. The MM model is further applied to a beta-hepta-peptide in methanol solution. The calculated NOE values and (3)J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non-natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of beta amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that beta-amino-acid based random copolymers can develop a high degree of amphiphilicity without regular three-dimensional structure.

Comparative study on inorganic Cl removal of municipal solid waste fly ash using different types and concentrations of organic acids.

In this study, different organic acids-such as citric, acetic, lactic, propionic, and butyric acid-were evaluated to ascertain the optimum leaching solvent for dechlorinating fly ash. Results suggest that the acid type, concentration, and interactions between both parameters contributed significantly to the variations in the efficiency of fly ash dechlorination. Simple main-effect analysis suggested that a higher acid concentration yields better dechlorination efficiency. However, improvements in dechlorination efficiency did not necessarily yield a low chlorine content leaching residue because in a specific acid concentration region, the increased acid concentration may also accelerate the mass reduction rate of the leaching residue. Experimental results also demonstrate that citric and acetic acid yield the highest dechlorination efficiency, followed by propionic and butyric acid. The least dechlorination efficiency of lactic acid could be attributed to the formation of precipitate (i.e. calcium lactate) which might cover the chlorides and reduce the contact area of intimal chlorides with the leaching solvent. Therefore, a specific concentration of organic matter fermentation broth rich in citric and acetic radicals may present itself as an ideal water substitute for fly ash dechlorination.

Design, synthesis and antiviral evaluation of novel acyclic phosphonate nucleotide analogs with triazolo[4,5-b]pyridine, imidazo[4,5-b]pyridine and imidazo[4,5-b]pyridin-2(3H)-one systems.

A new series of phosphonylated triazolo[4,5-b]pyridine (1-deaza-8-azapurine), imidazo[4,5-b]pyridine (1-deazapurine) and imidazo[4,5-b]pyridin-2(3H)-one (1-deazapurin-8-one) were synthesized from 2-chloro-3-nitropyridine and selected diethyl É·-aminoalkylphosphonates followed by reduction of the nitro group and cyclization. In the final step O,O-diethylphosphonates were transformed into the corresponding phosphonic acids. All synthesized compounds were evaluated in vitro for inhibitory activity against a broad variety of DNA and RNA viruses and their cytotoxic potencies were also established. Compound 12f showed marginal activity against cytomegalovirus Davis strain (EC50 = 76.47 µM) in human embryonic lung (HEL) cells while compounds 10g (EC50 = 52.53 µM) and 12l (EC50 = 61.70 µM) were minimally active against the varicella-zoster virus Oka strain in HEL cells. Compounds under investigation were not cytotoxic at the maximum concentration evaluated (100 µM).

Mutation of the active site carboxy-lysine (K70) of OXA-1 beta-lactamase results in a deacylation-deficient enzyme.

Class D beta-lactamases hydrolyze beta-lactam antibiotics by using an active site serine nucleophile to form a covalent acyl-enzyme intermediate and subsequently employ water to deacylate the beta-lactam and release product. Class D beta-lactamases are carboxylated on the epsilon-amino group of an active site lysine, with the resulting carbamate functional group serving as a general base. We discovered that substitutions of the active site serine and lysine in OXA-1 beta-lactamase, a monomeric class D enzyme, significantly disrupt catalytic turnover. Substitution of glycine for the nucleophilic serine (S67G) results in an enzyme that can still bind substrate but is unable to form a covalent acyl-enzyme intermediate. Substitution of the carboxylated lysine (K70), on the other hand, results in enzyme that can be acylated by substrate but is impaired with respect to deacylation. We employed the fluorescent penicillin BOCILLIN FL to show that three different substitutions for K70 (alanine, aspartate, and glutamate) lead to the accumulation of significant acyl-enzyme intermediate. Interestingly, BOCILLIN FL deacylation rates (t(1/2)) vary depending on the identity of the substituting residue, from approximately 60 min for K70A to undetectable deacylation for K70D. Tryptophan fluorescence spectroscopy was used to confirm that these results are applicable to natural (i.e., nonfluorescent) substrates. Deacylation by K70A, but not K70D or K70E, can be partially restored by the addition of short-chain carboxylic acid mimetics of the lysine carbamate. In conclusion, we establish the functional role of the carboxylated lysine in OXA-1 and highlight its specific role in acylation and deacylation.

Acid elution and one-dimensional shotgun analysis on an Orbitrap mass spectrometer: an application to drug affinity chromatography.

In this study, the target profile of the promiscuous kinase inhibitor bosutinib from whole cell K562 lysates was investigated by an improved chemical proteomic approach to identify natural binders. By (i) miniaturizing the drug pulldown method, (ii) introducing a 50 microm inner diameter (i.d.) analytical column for peptide separation, (iii) decreasing the inlet flow rate to 100 nL/minute, and (iv) analyzing the samples on an LTQ Orbitrap XL mass spectrometer, it was clearly demonstrated that the entire approach could be successfully down-scaled by a factor of 100, that is, equivalent to 2 x 10(6) K562 cells. The known major targets of bosutinib were still unequivocally identified in addition to 30 targets not previously identified by gel-based mass spectrometry in our laboratory. In total, 70 individual targets were identified by mass spectrometry across this study of which 19 had not been previously reported. The down-scaled technique was made feasible by eluting the proteins that interact with bosutinib with acid and analyzing the proteins by one-dimensional shotgun proteomics. Overall, these improvements should allow utilization of very limited amounts of patient material to generate a comprehensive and comparative profile of protein drug targets.