Determination of twenty pharmaceutical contaminants in soil using ultrasound-assisted extraction with gas chromatography-mass spectrometric detection.

In this paper, an analytical method for the simultaneous determination of twenty pharmaceuticals (eight non-steroidal anti-inflammatory drugs, five oestrogenic hormones, two antiepileptic drugs, two ß-blockers, and three antidepressants) in soils was developed. The optimal method included ultrasound-assisted extraction, a clean-up step on a silica gel column, derivatization using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) and 1% trimethylchlorosilane (TMCS) in pyridine and ethyl acetate (2:1:1, v/v/v) for 30 min at 60 °C, and determination by gas chromatography-mass spectrometry working in the selected ion monitoring mode. This affords good resolution, high sensitivity and reproducibility, and freedom from interferences even from complex matrices such as soils. The method detection limits ranged from 0.3 to 1.7 ng g-1, the intra-day precision represented as RSDs ranged from 1.1 to 10.0%, and the intra-day accuracy from 81.3 to 119.7%. The absolute recoveries of the target compounds were above 80%, except for valproic acid and diethylstilbestrol. The developed method was successfully applied in the analysis of the target compounds in soils collected in Poland. Among the 20 pharmaceuticals, 12 compounds were detected at least once in the soils. The determination of antiepileptic drugs, ß-blockers, and antidepressants was also performed for the first time.

Correction: Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains.

[This corrects the article DOI: 10.1371/journal.pone.0210874.].

Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains.

Ochrobactrum spp. are ubiquitous bacteria attracting growing attention as important members of microbiomes of plants and nematodes and as a source of enzymes for biotechnology. Strain Ochrobactrum sp. A44T was isolated from the rhizosphere of a field-grown potato in Gelderland, the Netherlands. The strain can interfere with quorum sensing (QS) of Gram-negative bacteria through inactivation of N-acyl homoserine lactones (AHLs) and protect plant tissue against soft rot pathogens, the virulence of which is governed by QS. Phylogenetic analysis based on 16S rRNA gene alone and concatenation of 16S rRNA gene and MLSA genes (groEL and gyrB) revealed that the closest relatives of A44T are O. grignonense OgA9aT, O. thiophenivorans DSM 7216T, O. pseudogrignonense CCUG 30717T, O. pituitosum CCUG 50899T, and O. rhizosphaerae PR17T. Genomes of all six type strains were sequenced, significantly expanding the possibility of genome-based analyses in Ochrobactrum spp. Average nucleotide identity (ANIb) and genome-to-genome distance (GGDC) values for A44T and the related strains were below the single species thresholds (95% and 70%, respectively), with the highest scores obtained for O. pituitosum CCUG 50899T (87.31%; 35.6%), O. rhizosphaerae PR17T (86.80%; 34.3%), and O. grignonense OgA9aT (86.30%; 33.6%). Distinction of A44T from the related type strains was supported by chemotaxonomic and biochemical analyses. Comparative genomics revealed that the core genome for the newly sequenced strains comprises 2731 genes, constituting 50-66% of each individual genome. Through phenotype-to-genotype study, we found that the non-motile strain O. thiophenivorans DSM 7216T lacks a cluster of genes related to flagella formation. Moreover, we explored the genetic background of distinct urease activity among the strains. Here, we propose to establish a novel species Ochrobactrum quorumnocens, with A44T as the type strain (= LMG 30544T = PCM 2957T).

The uniform structure of O-polysaccharides isolated from Dickeya solani strains of different origin.

O-polysaccharides were isolated from lipopolysaccharides obtained from four different strains of plant pathogenic bacteria belonging to the species Dickeya solani: two of them were isolated in Poland (IFB0099 and IFB0158), the third in Germany (IFB0223) and the last one, D. solani Type Strain IPO2222, originated from the Netherlands. In addition, the O-polysaccharide of a closely related species D. dadantii strain 3937 was isolated. The purified polysaccharides of the five strains were analyzed using NMR spectroscopy and chemical methods. Sugar and methylation analyses, including absolute configuration assignment, together with NMR data revealed that all O-polysaccharides tested are homopolymers of 6-deoxy-d-altrose (d-6dAlt) the following structure: →2)-ß-d-6dAltp-(1→.

Structural characterization of the O-polysaccharide isolated from Franconibacter helveticus LMG23732(T).

The bacterial strain Franconibacter helveticus LMG 23732(T) was previously misidentified as the neonatal pathogen Cronobacter zurichensis. O-polysaccharide (OPS) is a part of lipopolysaccharide (LPS), which is an important cell envelope compound of Gram-negative bacteria. OPS isolated from the bacterium Franconibacter helveticus LMG23732(T) was characterized by chemical analyses as well as 1D and 2D NMR experiments. Compositional analyses indicated the presence of glucose and unusual 6-deoxy sugar - 6-deoxy-talose (6-dTal). The studied strain produced OPS, which consists of 6-l-dTalp in main chain and terminal d-Glcp as a branch: This is the first structural determination of the OPS isolated from genus Franconibacter.

The structure of O-polysaccharides isolated from plant pathogenic bacteria Pectobacterium wasabiae IFB5408 and IFB5427.

O-Polysaccharides were isolated from the lipopolysaccharides of two strains of plant pathogenic bacteria Pectobacterium wasabiae isolated in Poland in 2013 (IFB5408 and IFB5427). The purified polysaccharides were analyzed using 1D and 2D NMR spectroscopy ((1)H, DQF-COSY, TOCSY, ROESY, HSQC, HSQC-TOCSY, and HMBC) and the chemical methods. Sugar and methylation analyses of native polysaccharides, absolute configuration assignment of constituent monosaccharides together with NMR spectroscopy data revealed that the chemical structures of both O-polysaccharides are the same.

Structural studies of O-polysaccharide isolated from Cronobacter sakazakii Sequence Type 12 from a case of neonatal necrotizing enterocolitis.

The O-polysaccharide (OPS) of Cronobacter sakazakii NTU 696 (Sequence Type 12) from a case of neonatal necrotizing enterocolitis was isolated from the polysaccharide fraction obtained after lipopolysaccharide (LPS) hydrolysis. Purified OPS was analyzed by NMR spectroscopy ((1)H, COSY, TOCSY, NOESY, HSQC, HSQC-TOCSY and HMBC experiments) and chemical methods. Obtained monosaccharide derivatives analyzed by gas chromatography and gas chromatography-mass spectrometry allowed the identification of six sugar components. Performed experiments enabled to establish a structure of the OPS repeating unit of C. sakazakii NTU 696, as: [structure: see text].

The structure of O-polysaccharide isolated from Cronobacter universalis NCTC 9529T.

The O-polysaccharide (OPS) was isolated from Cronobacter universalis NCTC 9529(T), a new species in the genus Cronobacter, which was created by the reclassification of the species Enterobacter sakazakii. Purified polysaccharide was analyzed by NMR spectroscopy ((1)H, COSY, TOCSY, ROESY, HSQC, and HSQC-TOCSY) and chemical methods. The monosaccharide derivatives were analyzed by gas chromatography and gas chromatography-mass spectrometry. These experiments enabled the type and number of monosaccharides in the repeating unit of OPS, their positions of linkages, and absolute configuration to be determined. Together the chemical analysis established a structure of the OPS of C. universalis NCTC 9529(T). [structure: see text]. OPS isolated from C. universalis was structurally characterized for the first time.

Detection of denatonium benzoate (bitrex) remnants in noncommercial alcoholic beverages by Raman spectroscopy.

Illegal alcoholic beverages are often introduced into market using cheap technical alcohol, which is contaminated by denatonium benzoate (Bitrex) of very small concentration. Bitrex is the most bitter chemical compound and has to be removed before alcohol consumption. The home-made methods utilize sodium hypochlorite to disintegrate particles of denatonium benzoate in alcohol and to remove bitter taste before trading. In this experimental studies, we propose a novel method that detects in a fast way the remnants of denatonium benzoate in dubious alcohol samples by Raman spectroscopy. This method applies a portable Raman spectrometer of excitation wavelength 785 nm and utilizes the effect of surface-enhanced Raman spectroscopy (SERS) to recognize the suspected alcoholic beverages. High effectiveness (over 98%) of YES/NO classification of the investigated samples was observed when the nonlinear algorithm support vector machine (SVM) was exploited at carefully adjusted detection parameters. The method can identify illicit alcohol within minutes.

A new silylation reagent dimethyl(3,3,3-trifluoropropyl)silyldiethylamine for the analysis of estrogenic compounds by gas chromatography-mass spectrometry.

In this study we applied DIMETRIS (dimethyl(3,3,3-trifluoropropyl)silyldiethylamine), a new silylating reagent, to derivative natural estrogens such as estrone (E1), 17ß-estradiol (E2) and estriol (E3), as well as the synthetic 17α-ethinylestradiol (EE2) and the non-steroid diethylstilbestrol (DES). Its derivatizing properties were compared with those of the commonly used mixture of BSTFA (N,O-bis(trimethylsilyl)trifluoroacetamide)+1% trimethylchlorosilane (TMCS) and with MTBSTFA (N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide). The use of DIMETRIS for the silylation all of them is reported for the first time. The nucleophilic properties of DIMETRIS were found to be superior to those of MTBSTFA, but slightly inferior to those of BSTFA. It was used to derivatize steroid (E1, E2, E3 and EE2) and non-steroid (DES) estrogens at 30°C prior to GC/MS analysis. These DMTFPS-derivatives exhibited good separation (low retention times despite the high molecular masses) and ionization properties in GC/MS analyses (the highest relative response factors for DMTFPS-derivatives among those tested). However, DIMETRIS and MTBSTFA (which produce mono-O-silyl derivatives of EE2) should not be used for the simultaneous analysis of EE2 and E1. Only a mixture of BSTFA+1% TMCS in pyridine, which generates the fully derivatized EE2 product (stable in GC injector), permits the determination of these two estrogenic compounds during one GC-MS run. On the other hand, because DIMETRIS requires a lower derivatization temperature than BSTFA, it could be very useful for the derivatization of thermally unstable estrogenic compounds. In the next step of this study, the SPE-GC-MS method based on DIMETRIS derivatization for the analysis of DES, E2 and E3 in aqueous samples was evaluated and validated. The MQL values: 1.4, 1.6 and 1.5ngL(-1) for DES, E2 and E3, respectively, proved its suitability to determine target compounds in environmental samples. Finally, the proposed method was successfully applied to the analysis of selected estrogenic compounds in real seawater and wastewater samples in Poland.

Chemometric optimization of derivatization reactions prior to gas chromatography-mass spectrometry analysis.

Derivatization is a methodological technique that can be used to make an organic compound more suitable for qualitative and/or quantitative analysis (e.g. pharmaceuticals). However, many analysts try to avoid this analytical procedure as it is time-consuming and labour-intensive. On the other hand, an inter-laboratory study demonstrated that with regard to sensitivity and measurement uncertainty, gas chromatography coupled to mass-spectrometry was superior to liquid chromatography coupled to mass spectrometry for the trace analysis of organic compounds in matrices of greater complexity. In our previous paper (Kumirska et al., J. Chemometr. 25 (2011) 636-643) we suggested using principal component analysis (PCA) to optimize the derivatization of six compounds (5 oestrogenic steroids and diethylstilbestrol) prior to GC-MS analysis. In the present work we applied a highly sophisticated model - 24 pharmaceuticals derived from six classes of drugs. The efficiency of different derivatization reactions was evaluated by PCA and compared with that obtained from cluster analysis (CA), the latter method being applied in this context for the first time. Derivatization using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) and 1% trimethylchlorosilane (TMCS) in pyridine and ethyl acetate (2:1:1, v/v/v) for 30min at 60°C was found to be optimal. The SPE-GC-MS method was also validated and successfully applied to the analysis of selected pharmaceuticals in wastewater and surface waters in Poland.

Chemical structure of the O-polysaccharides isolated from Cronobacter turicensis sequence type 5 strains 57, 564, and 566.

The Cronobacter spp. are Gram-negative bacterial pathogens that can cause infections in all age groups, and have a high mortality rate in neonates due to necrotizing enterocolitis and meningitis. Recent genotyping studies have revealed a strong clonal lineage in the genus, but this has not been compared with physiological traits. The O-polysaccharides (OPS) were isolated from three C. turicensis sequence type 5 strains (57, 564, and 566) and structurally characterized using (1)H and (13)C NMR spectroscopy, including two-dimensional DQF-COSY, TOCSY, ROESY, and HSQC analysis. Further compositional determination was undertaken using classical chemical methods followed by GLC, and GLC-MS analysis. The repeating unit of the isolated O-polysaccharides consists of GlcNAc, Rha, Glc, and had the structure shown below and therefore complemented the sequence type. [structure: see text].

Immunochemical studies of Salmonella Dakar and Salmonella Telaviv O-antigens (serogroup O:28).

Salmonella Dakar and Salmonella Telaviv bacteria belong to serogroup O:28, which represents 107 serovars and possesses only the epitope O28. Salmonella Telaviv has the subfactors O28(1) and O28(2) , whereas S. Dakar has O28(1) and O28(3) . So far, only limited serological and immunological information for this serogroup is available in the literature. Knowledge of the structures of their O-polysaccharides and the immunochemical investigations performed in this work allowed to reveal the nature of subfactor O28(1) as attributed to the presence of 3-linked (or 3,4-disubstituted) α-d-GalpNAc in the main chains of S. Dakar and S. Telaviv O-polysaccharides. An explanation for the cross-reactions between Salmonella enterica O28 O-antigens and other Salmonella O-polysaccharides and their structural similarity to Escherichia coli O-serogroups is also given.

Chemical structure of the O-polysaccharide isolated from Pectobacterium atrosepticum SCRI 1039.

The lipopolysaccharide (LPS) of the bacterium Pectobacterium atrosepticum SCRI 1039 was hydrolyzed and the products were separated. A study of the obtained O-polysaccharide by means of chemical methods, GLC, GLC-MS, and NMR spectroscopy allowed us to identify a branched polymer with a pentasaccharide repeating unit of the structure shown below, in which the fucose residue was partially O-acetylated at C-2, C-3 or C-4.

Chemical structure of wall teichoic acid isolated from Enterococcus faecium strain U0317.

Wall teichoic acid (WTA) was isolated from Enterococcus faecium strain U0317 and structurally characterized using (1)H, (13)C, and (31)P NMR spectroscopy, including two-dimensional COSY, TOCSY, ROESY, HMQC, and HMBC experiments. Further compositional determination was undertaken using classical chemical methods and HF treatment followed by GLC and GLC-MS analyses. The repeating unit of WTA consisted of two residues of 2-acetamido-2-deoxy-D-galactose, glycerol (Gro), and phosphate, and has the structure shown below: [See formula in text].

Unexpected photoproduct generated via the acetone-sensitized photolysis of 5-bromo-2'-deoxyuridine in a water/isopropanol solution: experimental and computational studies.

The acetone-sensitized photolysis of 5-bromo-2'-deoxyuridine (5-BrdU) in a water/isopropanol solution with 300 nm photons leads to the formation of 2'-deoxyuridine (dU) and a comparable amount of another photoproduct that has not been reported in the literature so far. The negative and positive mass spectra recorded for this species indicate that they originate from the molecular mass of 286 Da, which corresponds to an adduct of 2'-deoxyuridine and 2-propanol. Quantum chemical calculations carried out at the DFT and TDDFT levels reveal both the structure and the UV spectrum of that adduct. The latter computational characteristic matches well the experimental UV spectrum of the new photoproduct. Our findings indicate that the acetone-sensitized photolysis of 5-BrdU is more complicated than has hitherto been assumed. Nevertheless, since electron transfer is one of the pathways responsible for 5-BrdU decay, acetone-sensitized photolysis of the halogen derivatives of nucleobases could be a convenient tool for studying their radiosensitivity in aqueous solutions.

Application of spectroscopic methods for structural analysis of chitin and chitosan.

Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds.

Structure of the O-polysaccharide isolated from Cronobacter sakazakii 767.

The Cronobacter spp., previously known as Enterobacter sakazakii, are Gram-negative enterobacterial pathogens that can cause necrotizing enterocolitis, meningitis, and septicemia with a high mortality rate in neonates. The O-specific polysaccharide (O-PS) was isolated from Cronobacter sakazakii strain 767 and structurally characterized using (1)H and (13)C NMR spectroscopy, including two-dimensional DQF-COSY, TOCSY, ROESY, HSQC, and HMBC experiments. Further compositional determination was undertaken using classical chemical methods followed by GLC, and GLC-MS analysis. The repeating unit of O-PS isolated from C. sakazakii 767 was a branched heptasaccharide composed of l-Rha, d-Glc, d-GlcNAc, and d-GalA, and had the structure shown below. One of the Rha residues was partially O-acetylated at C-4. C. sakazakii 767 was originally isolated from a fatal neonatal meningitic case, and the structure of its O-PS significantly differs from the O-PS structures previously described for Cronobacter spp.

Smith degradation of the O-antigenic polysaccharide of Salmonella Dakar: structural studies of the products.

Two different oligosaccharides were obtained from the Smith degradation of the O-polysaccharide isolated from the lipopolysaccharide of Salmonella Dakar. The structures of these oligosaccharides were investigated by chemical analysis, NMR spectroscopy and MALDI-TOF mass spectrometry. The following structures of these products were determined: alpha-D-GalpNAc-(1-->4)-alpha-D-Quip3NAc-(1-->3)-alpha-L-Rhap-(1-->2)-threitol and [Formula: see text] where Quip3NAc is 3-acetamido-3,6-dideoxyglucose. The reaction products confirmed the structure of the repeating unit of the Salmonella Dakar O-polysaccharide reported previously [Kumirska, J.; Szafranek, J.; Czerwicka, M.; Paszkiewicz, M.; Dziadziuszko, H.; Kunikowska, D.; Stepnowski, P. Carbohydr. Res. 2007,342, 2138-2143].

The structure of the O-polysaccharide isolated from the lipopolysaccharide of Salmonella Dakar (serogroup O:28).

The structure of the O-antigenic part of the lipopolysaccharide (LPS) of Salmonella Dakar was analysed using chemical methods, NMR spectroscopy and mass spectrometry. The following structure for the repeating unit of the O-polysaccharide was determined: [see text] where Quip3NAc is 3-acetamido-3,6-dideoxyglucose. This is the first published structure of the O-polysaccharides from 101 serotypes of Salmonella bacteria belonging to serogroup O:28 (formerly M) in the Kauffmann-White scheme.