A Paleogenomic Algorithm for Reconstruction of Ancient Operons from Complete Microbial Genome Sequences

Operons, or co-transcribed and co-regulated contiguous sets of genes, in microbial genomes are poorly conserved across different genomes due to gene fusion, deletion, duplication and other genome shuffling processes. The currently available genomes are the results of numerous reshuf-     

Trichloroisocyanuric Acid–KF as an Efficient Reagent for One-Pot Synthesis of Dialkylfluorophosphates from Dialkylphosphites

Trichloroisocyanuric acid–KF afforded dialkylfluorophosphates from dialkylphosphites at room temperature through a facile electrophilic–nucleophilic metathesis.     

Multiresidue Method for the Determination of Organophosphorus Pesticides in Still Wine and Fortified Wine Using Solid-Phase Microextraction and Gas Chromatography – Tandem Mass Spectrometry

A SPME-GC-MS/MS method for the determination of eight organophosphorus pesticides (azinphos-methyl, chlorpyriphos, chlorpyriphos-methyl, diazinon, fenitrothion, fenthion, malathion, and methidathion) in still and fortified wine was developed. The extraction procedure is simple, solvent free, and without any sample pretreatment. Limits of detection (LOD) and quantitation (LOQ) values in the range 0.1–14.3 µg/L and 0.2–43.3 µg/L, respectively, were obtained. The LOQ values are below the maximum residue levels (MRLs) established by European Regulation for grapes, with the exception of methidathion. Coefficients of correlation (R²) higher than 0.99 were obtained for the majority of the pesticides, in all different wines analyzed.     

Bengal gram seed husk as an adsorbent for the removal of dyes from aqueous solutions – Column studies

A continuous fixed bed (column) study was carried out by using seed husk of Bengal gram (Cicer arietinum) (SHBG) as a biosorbent for the removal of direct dye, Congo red (CR) from aqueous solutions. The effects of important factors, such as the value of initial pH, the flow rate, the influent concentration of CR, bed depth, particle size of SHBG, foreign ions and regeneration of CR were studied. The effect of similar type of direct dyes like direct turquoise blue 86 (DTB) and direct black 38 (DB) on the adsorption of CR in column containing SHBG is also studied by keeping other parameters constant. The studies confirmed that the breakthrough curves were dependent on flow rate, initial dye concentration, size of SHBG, initial pH of solution of CR and bed depth. The bed depth service time analysis (BDST) model was applied at different bed depths to predict the breakthrough curves. The model is found suitable for describing the biosorption process of the dynamic behaviour of the SHBG column and the data were in good agreement with BDST model. When the flow rate was 0.67 mL/min and the influent concentration of CR was mg L⁻¹, the column capacity was 6.572 mg g⁻¹. The removal capacity of SHBG was more in case of CR (6.572 mg g⁻¹) compared to other similar direct dyes of DTB (1.984 mg g⁻¹) and DB (1.612 mg g⁻¹). The removal of CR was enhanced in the presence of foreign ion potassium (8.308 mg g⁻¹) and decreased in the presence of calcium (5.58 mg g⁻¹). 120 ml of acetone is required for the completion of regeneration of the column and the total amount of CR recovered in this case. All the results suggested SHBG as a potential adsorbent for removal of CR from aqueous solution so that the rate of bio-sorption process is rapid.     

Loss of 45 Da from a<Subscript>2</Subscript> Ions and Preferential Loss of 48 Da from a<Subscript>2</Subscript> Ions Containing Methionine in Peptide Ion Tandem Mass Spectra

While analyzing tandem mass spectra of tryptic tripeptides, intense unassigned peaks were observed, corresponding to neutral loss of 45 Da from a₂ ions. This process was confirmed by MS³ experiments. Based on exact mass analysis, the loss was ascribed to (NH₃ + CO) or formamide. The proposed mechanism involves a cyclic form of the a₂ ions. The structure of the a₂ − 45 ions was confirmed by their fragmentation in MS³ experiments. Loss of (NH₃ + CO) from the a₂ ions occurs in competition with other paths, such as the loss of H₂O or the formation of immonium ions. However, if the a₂ ion contains methionine, a neutral loss of 48 Da (ascribed to CH₃SH) predominates, and is followed by the loss of (NH₃ + CO). These processes were confirmed by MS³ experiments. The intensity of the a₂ − 48 peak formed from XaaMet has a maximum value of 42% (of the total intensity of all ions) for Xaa=Gly, varies between 15% and 40% for most other Xaa residues, is lower for residues that can undergo loss of water or ammonia, and is very low for Lys or Arg. When the order of the residues is reversed to MetXaa, the loss of 48 Da is much smaller. This effect can be used to determine the sequence of b₂ ions containing Met in proteomic studies. Considerable loss of CH₃SH is observed from doubly protonated tryptic tripeptides with N-terminal Met, but the loss is much less when they are singly protonated or when Met is in the center position.     

Development and Validation of a Simple and Efficient Method for the Determination of Pendimethalin and Its Metabolite M455H001 in Soil by Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS)

A new analytical method has been developed and described for the rapid determination of pendimethalin and its major metabolite M455H001 in soil by liquid chromatography coupled with ion-spray tandem mass spectrometry (LC-MS/MS) after a single acidic solvent extraction. The chromatographic separation of the analytes was achieved using a Zorbax C18 reversed phase column and water/0.1% formic acid and methanol as the mobile phase at a flow rate of 0.2?mL?min^?1. The recoveries of the method ranged from 78.8% to 119.8% for pendimethalin and from 73.7% to 108.8% for M455H001, and the relative standard deviation was lower than 16% for both analytes. The validated limit of quantification was 0.01?µg?g^?1 soil dry weight for both compounds. The matrix effects were evaluated and were less than 20% for both substances in the examined soil samples. It is concluded that the method is easy, with reasonable consumption of reagents, characterized by reliability and sensitivity, and therefore, it is suitable for monitoring the levels of pendimethalin and its major metabolite M455H001 in soils.     

Features of the First and Second Order Electrospray Ionization Mass Spectra for Salt-Like Products Derived from Monools and Diols Using Combined Reagents Based on ω-Bromoacyl Chlorides and Nitrogen Bases

Derivatization by composite reagents based on ω-bromoacyl chlorides [ClCO(C₂) _n Br (n = 1–4)] and pyridine was applied to study aliphatic and alicyclic alcohols and diols by ordinary and tandem electrospray ionization (ESI) mass spectrometry. The applied derivatization involves the simultaneous acylation of hydroxyl groups with an acyl chloride moiety and the quaternization of pyridine with a terminal bromoalkyl group. Under the ESI conditions, quaternary salts produce corresponding mono and diammonium cations, which are detected in the first-order mass spectra. Collision-induced dissociation (CID) of primary cations generated from monool derivatives gives rise to ammonium cations of the corresponding acids HOOC(CH₂) _n –N⁺(C₅H₅). The CID of primary dications affords the same cations which are also eliminated from dications to form mono-charged fragments.