Multiplex identification of drug‐resistant Gram‐positive pathogens using stuffer‐free MLPA system

Early detection of pathogens from blood and identification of their drug resistance are essential for sepsis management. However, conventional culture‐based methods require relatively longer time to identify drug‐resistant pathogens, which delays therapeutic decisions. For precise multiplex detection of drug‐resistant Gram‐positive pathogens, we developed a method by using stuffer‐free multiplex ligation‐dependent probe amplification (MLPA) coupled with high‐resolution CE single‐strand conformation polymorphisms (CE‐SSCP) system. We designed three probe sets for genes specific to Gram‐positive species (Staphylococcus aureus: nuc, Enterococcus faecium: sodA, and Streptococcus pneumoniae: lytA) and two sets for genes associated with drug resistance (mecA and vanA) to discriminate major Gram‐positive pathogens with the resistance. A total of 94 different strains (34 reference strains and 60 clinical isolates) were used to validate this method and strain‐specific peaks were successfully observed for all the strains. To improve sensitivity of the method, a target‐specific preamplification step was introduced and, consequently, the sensitivity increased from 10 pg to 100 fg. We also reduced a total assay time to 8 h by optimizing hybridization time without compromising test sensitivity. Taken together, our multiplex detection system can improve detection of drug‐resistant Gram‐positive pathogens from sepsis patients’ blood.     

Capillary electrophoresis for fast detection of heterogeneous population in colistin‐resistant Gram‐negative bacteria

It has been shown that diverse strains of bacteria can be separated according to their characteristic surface properties by means of CE. We employed here this analytical technique to the study of colistin‐resistance in Gram‐negative bacteria, which involves the selection of mutants with modified outer membrane composition resulting in changes of surface cell properties. In the same way as with molecular entities, we performed firstly the validation of an ITP‐based CE method for three common pathogenic Gram‐negative bacteria namely Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Secondly, we compared the electrophoretic profiles of bacterial samples from a colistin‐susceptible clinical isolate of K. pneumoniae and from the corresponding colistin‐resistant derivative. By a simple CE run taking a few minutes, the coexistence of several bacterial subpopulations in the colistin‐resistant derivative was clearly evidenced. This work encourages further research that would allow applications of CE in clinical laboratory for a daily monitoring of bacterial population in cared patients when “last‐chance” colistin treatment is initiated against multidrug‐resistant bacteria.     

GenoMass ‐ a computer software for automated identification of oligonucleotide DNA adducts from LC‐MS analysis of DNA digests

In the investigation of oligonucleotides, DNA and their adducts by LC‐MS, a myriad of data are generated that make manual data processing quite difficult. This paper describes a ‘reversed pseudo‐combinatorial’ approach for fragment identification and the software implementation of this approach. Combinatorial isomer libraries are generated in silico to represent the digestion products of oligonucleotides, DNA or DNA adducts of various sizes. The software automatically calculates ion masses of each isomeric segment of the library, searches for them in complicated LC‐MS data, lists their intensities and plots extracted ion chromatograms (EIC). This customized new data analysis tool has enabled a study of the enzymatic behavior of a nuclease system in the digestion of normal and adducted DNA, and in the recognition of oligomers containing a carcinogen bound to a nucleobase. The software program potentially can be further expanded to postulate unknown DNA sequences and recognize the adduction sites. Copyright © 2008 John Wiley & Sons, Ltd.     

Fragmentation of negative ions from N‐linked carbohydrates,Part 4. Fragmentation of complex glycans lacking substitution on the 6‐antenna

Negative ion CID spectra of N‐linked glycans released from glycoproteins contain many ions that are diagnostic for specific structural features such as the detailed arrangement of antennae and the location of fucose residues. Identification of such ions requires reference glycans that are often difficult to acquire in a pure state. The recent acquisition of a sample of N‐glycans from a patient lacking the enzyme N‐acetylglucosaminyltransferase‐2 provided an opportunity to investigate fragmentation of glycans lacking a 6‐antenna. These glycans contained one or two galactose‐N‐acetylglucosamine‐chains attached to the 3‐linked mannose residue of the trimannosyl‐chitobiose core with and without fucose substitution. The spectra from the patient sample clearly defined the antenna distribution and showed striking differences from the spectra of isomeric compounds obtained from normal subjects. Furthermore, they provided additional information on previously identified antenna‐specific fragment ions and indicated the presence of additional ions that were diagnostic of fucose substitution. Glycans obtained from such enzyme‐deficient patients can, thus, be a valuable way of obtaining spectra of specific isomers in a relatively pure state for interpretation of mass spectra. Copyright © 2010 John Wiley & Sons, Ltd.     

Metabolic profiling for the identification of Huntington biomarkers by on‐line solid‐phase extraction capillary electrophoresis mass spectrometry combined with advanced data analysis tools

In this work, an untargeted metabolomic approach based on sensitive analysis by on‐line solid‐phase extraction capillary electrophoresis mass spectrometry (SPE‐CE‐MS) in combination with multivariate data analysis is proposed as an efficient method for the identification of biomarkers of Huntington's disease (HD) progression in plasma. For this purpose, plasma samples from wild‐type (wt) and HD (R6/1) mice of different ages (8, 12, and 30 weeks), were analyzed by C₁₈‐SPE‐CE‐MS in order to obtain the characteristic electrophoretic profiles of low molecular mass compounds. Then, multivariate curve resolution alternating least squares (MCR‐ALS) was applied to the multiple full scan MS datasets. This strategy permitted the resolution of a large number of metabolites being characterized by their electrophoretic peaks and their corresponding mass spectra. A total number of 29 compounds were relevant to discriminate between wt and HD plasma samples, as well as to follow‐up the HD progression. The intracellular signaling was found to be the most affected metabolic pathway in HD mice after 12 weeks of birth, when mice already showed motor coordination deficiencies and cognitive decline. This fact agreed with the atrophy and dysfunction of specific neurons, loss of several types of receptors, and changed expression of neurotransmitters.     

Interaction identification of Zif268 and TATAZF proteins with GC‐/AT‐rich DNA sequence: A theoretical study

Molecular dynamics (MD) simulations for Zif268 (a zinc‐finger‐protein binding specifically to the GC‐rich DNA)‐d(A₁G₂C₃G₄T₅G₆G₇G₈C₉A₁₀C₁₁)₂ and TATA_ZF (a zinc‐finger‐protein recognizing the AT‐rich DNA)‐d(A₁C₂G₃C₄T₅A₆T₇A₈A₉A₁₀A₁₁G₁₂G₁₃)₂ complexes have been performed for investigating the DNA binding affinities and specific recognitions of zinc fingers to GC‐rich and AT‐rich DNA sequences. The binding free energies for the two systems have been further analyzed by using the molecular mechanics Poisson‐Boltzmann surface area (MM‐PBSA) method. The calculations of the binding free energies reveal that the affinity energy of Zif268‐DNA complex is larger than that of TATA_ZF‐DNA one. The affinity between the zinc‐finger‐protein and DNA is mainly driven by more favorable van‐der‐Waals and nonpolar/solvation interactions in both complexes. However, the affinity energy difference of the two binding systems is mainly caused by the difference of van‐der‐Waals interactions and entropy components. The decomposition analysis of MM‐PBSA free energies on each residue of the proteins predicts that the interactions between the residues with the positive charges and DNA favor the binding process; while the interactions between the residues with the negative charges and DNA behave in the opposite way. The interhydrogen‐bonds at the protein‐DNA interface and the induced intrafinger hydrogen bonds between the residues of protein for the Zif268‐DNA complex have been identified at some key contact sites. However, only the interhydrogen‐bonds between the residues of protein and DNA for TATA_ZF‐DNA complex have been found. The interactions of hydrogen‐bonds, electrostatistics and van‐der‐Waals type at some new contact sites have been identified. Moreover, the recognition characteristics of the two studied zinc‐finger‐proteins have also been discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Competitive homolytic and heterolytic decomposition pathways of gas‐phase negative ions generated from aminobenzoate esters

An alkyl‐radical loss and an alkene loss are two competitive fragmentation pathways that deprotonated aminobenzoate esters undergo upon activation under mass spectrometric conditions. For the meta and para isomers, the alkyl‐radical loss by a homolytic cleavage of the alkyl‐oxygen bond of the ester moiety is the predominant fragmentation pathway, while the contribution from the alkene elimination by a heterolytic pathway is less significant. In contrast, owing to a pronounced charge‐mediated ortho effect, the alkene loss becomes the predominant pathway for the ortho isomers of ethyl and higher esters. Results from isotope‐labeled compounds confirmed that the alkene loss proceeds by a specific γ‐hydrogen transfer mechanism that resembles the McLafferty rearrangement for radical cations. Even for the para compounds, if the alkoxide moiety bears structural motifs required for the elimination of a more stable alkene molecule, the heterolytic pathway becomes the predominant pathway. For example, in the spectrum of deprotonated 2‐phenylethyl 4‐aminobenzoate, m/z 136 peak is the base peak because the alkene eliminated is styrene. Owing to the fact that all deprotonated aminobenzoate esters, irrespective of the size of the alkoxy group, upon activation fragment to form an m/z 135 ion, aminobenzoate esters in mixtures can be quantified by precursor ion discovery mass spectrometric experiments. Copyright © 2016 John Wiley & Sons, Ltd.     

Application of negative ion MS/MS to the identification of N-glycans released from carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1)

Structures of N-glycans released from rat CEACAM1 expressed in human embryonic kidney cells were determined by MALDI and negative ion nanospray MS/MS techniques. The major carbohydrates were bi-, tri- and tetra-antennary complex glycans with and without sialic acid, fucose and bisecting GlcNAc residues. High-mannose glycans, predominantly Man(5)GlcNAc(2), were also found. The negative ion fragmentation technique easily identified the branching pattern of the triantennary glycans (mainly branched on the 6-antenna) and the presence of 'bisecting' GlcNAc residues (attached to the 4-position of the core mannose), features that are difficult to determine by traditional techniques. Sialic acids were in both alpha2-3 and alpha2-6 linkage as determined by MALDI-TOF MS following linkage-specific derivatization.     

Characterization of an exception to the ‘even‐electron rule’ upon low‐energy collision induced decomposition in negative ion electrospray tandem mass spectrometry

Electrospray‐generated precursor ions usually follow the ‘even‐electron rule’ and yield ‘closed shell’ fragment ions. We characterize an exception to the ‘even‐electron rule.’ In negative ion electrospray mass spectrometry (ES‐MS), 2‐(ethoxymethoxy)‐3‐hydroxyphenol (2‐hydroxyl protected pyrogallol) easily formed a deprotonated molecular ion (M‐H)^? at m/z 183. Upon low‐energy collision induced decomposition (CID), the m/z 183 precursor yielded a radical ion at m/z 124 as the base peak. The radical anion at m/z 124 was still the major fragment at all tested collision energies between 0 and 50 eV (E_lab). Supported by computational studies, the appearance of the radical anion at m/z 124 as the major product ion can be attributed to the combination of a low reverse activation barrier and resonance stabilization of the product ions. Furthermore, our data lead to the proposal of a novel alternative radical formation pathway in the protection group removal of pyrogallol. Copyright © 2009 John Wiley & Sons, Ltd.     

Energy‐surfaces from the upper bound of the Pauli kinetic energy

Based on the Kohn–Sham Pauli potential and the Kohn–Sham electron density, the upper bound of the Pauli kinetic energy is tested as a suitable replacement for the exact Pauli kinetic energy for application in orbital‐free density functional calculations. It is found that bond lengths for strong and moderately bound systems can be qualitatively predicted, but with a systematic shift toward larger bond distances with a relative error of 6% up to 30%. Angular dependence of the energy‐surface cannot be modeled with the proposed functional. Therefore, the upper bound model is the first parameter‐free functional expression for the kinetic energy that is able to qualitatively reproduce binding curves with respect to bond distortions. © 2016 Wiley Periodicals, Inc.     

Desulfurization of phosphorothioate oligonucleotides via the sulfur‐by‐oxygen replacement induced by the hydroxyl radical during negative electrospray ionization mass spectrometry

While the occurrence of desulfurization of phosphorothioate oligonucleotides in solution is well established, this study represents the first attempt to investigate the basis of the unexpected desulfurization via the net sulfur‐by‐oxygen (S‐O) replacement during negative electrospray ionization (ESI). The current work, facilitated by quantitative mass deconvolution, demonstrates that considerable desulfurization can take place even under common negative ESI operating conditions. The extent of desulfurization is dependent on the molar phosphorothioate oligonucleotide‐to‐hydroxyl radical ratio, which is consistent with the corona discharge‐induced origin of the hydroxyl radical leading to the S‐O replacement. This hypothesis is supported by the fact that an increase of the high‐performance liquid chromatography (HPLC) flow rate and the on‐column concentration of a phosphorothioate oligonucleotide, as well as a decrease of the electrospray voltage reduce the degree of desulfurization. Comparative LC‐tandem mass spectrometry (MS/MS) sequencing of a phosphorothioate oligonucleotide and its corresponding desulfurization product revealed evidence that the S‐O replacement occurs at multiple phosphorothioate internucleotide linkage sites. In practice, the most convenient and effective strategy for minimizing this P = O artifact is to increase the LC flow rate and the on‐column concentration of phosphorothioate oligonucleotides. Another approach to mitigate possible detrimental effects of the undesired desulfurization is to operate the ESI source at a very low electrospray voltage to diminish the corona discharge; however this will significantly compromise sensitivity when analyzing the low‐level P = O impurities in phosphorothioate oligonucleotides. Copyright © 2012 John Wiley & Sons, Ltd.     

Zwitterionic Salts from the Reaction of Symmetrical and Unsymmetrical (thio)Barbituric Acids with 2‐Pyridinecarbaldehyde under Solvent‐free Condition

A simple and efficient synthesis for the preparation of unusual charge‐separated pyridinium (thio)barbiturate zwitterion derivatives was achieved via a one‐pot reaction of (thio)barbituric acid derivatives and 2‐pyridinecarbaldehyde under solvent‐free condition and also in methanol under refluxing. The structure of the compounds was confirmed by ¹H NMR, ¹³C NMR, FT‐IR, mass and X‐ray analysis. The mechanism of the formation is discussed. Instead, no related pyridinium zwitterion was afforded from the reaction between dimedone and 2‐pyridinecarbaldehyde under the same conditions and its xanthene derivative was obtained.     

GC‐MSn and LC‐MS/MS couplings for the identification of degradation products resulting from the ozonation treatment of Acetochlor

The degradation of the chloracetamide herbicide acetochlor has been studied under simulated ozonation treatment plant conditions. The degradation of acetochlor included the formation of several degradation products that were identified using GC/ion‐trap mass spectrometry with EI and CI and HPLC/electrospray‐QqTOF mass spectrometry. Thirteen ozonation products of acetochlor have been identified. Ozonation of the deuterated herbicide combined to MSⁿ and high‐resolution mass measurement allowed effective characterization of the degradation products. At the exception of one of them, the product B (2‐chloro‐2', ethyl‐6', methyl‐acetanilide), none of the identified degradation products has been already reported in the literature. Post‐ozonation kinetics studies revealed that the concentrations of most degradation products evolved noticeably with time, particularly during the first hours following the ozonation treatment. This raises concerns about the fate of degradation products in the effluents of treatment plants and suggests the need for a better control on these products if their toxicity was demonstrated. Copyright © 2012 John Wiley & Sons, Ltd.     

Capacitive Properties of the Binder‐Free Electrode Prepared from Carbon Derived from Cotton and Reduced Graphene Oxide

The binder‐free composite films of reduced graphene oxide (rGO ) and activated carbon derived from cotton (aCFC ) have been fabricated and used as electrodes for electrochemical capacitors (ECs ) to avoid the decrease of capacitive performance in traditional process caused by the additional binder. The optimal aCFC is prepared at 850 °C when the mass ratio of carbon and potassium hydroxide is 1 to 4. The optimal composite film prepared from the mass ratio of aCFC /GO =2/1 exhibits porous structure, and has a specific surface area of 849.6 m²•g⁻¹ and a total pore volume of 0.61 mL •g⁻¹. Based on the two‐electrode system testing in 6.0 mol/L KOH electrolyte, the optimal composite has specific capacitance of about 202 F•g⁻¹, 374 mF •cm⁻² and 116 F•cm⁻³ in terms of mass, area and volume, and shows excellent rate capability and good cyclic stability (91.7% retention of the initial capacitance after 5000 cycles). Furthermore, the assembled solid‐state ECs by using KOH /polyvinyl alcohol as electrolyte show good mechanical stability and capacitive performances after repeated bending cycles. It is proved that this method is effective to fabricate binder‐free electrodes for ECs and will open up a novel route for the reuse of waste cotton.     

Facile preparation of boronic acid‐functionalized magnetic nanoparticles with a high capacity and their use in the enrichment of cis‐diol‐containing compounds from plasma

The use of bronate affinity adsorbents is a new separation method that appeared recently with great potential for specific extraction of cis‐diol‐containing compounds. In this work,a new strategy for the facile construction of boronic acid‐functionalized Fe₃O₄ magnetic nanoparticles (Fe₃O₄@FPBA MNPs) with a high capacity was described. The extraction capacity of the Fe₃O₄@FPBA MNPs was determined to be 66.0 ± 2.7 µmol/g for catechol and 80.6 ± 2.0 µmol/g for dopamine, being higher than that for the reported methods. The Fe₃O₄@FPBA MNPs were used to extract four cis‐diol drugs: caffeic acid isopropyl ester, caffic acid bornyl ester, isopropyl 3‐(3,4‐dihydroxyphenyl)‐2‐hydroxypropanoate and 3‐(3, 4‐dihydroxyphenyl)‐2‐hydroxylpropionic acid – from the spiked rabbit plasma, and the recoveries of four drugs were between 87.29 and104.37% with relative standard deviations ranging from 1.34 to 8.81%. Under the most favorable conditions, the solid‐phase extraction combined with HPLC‐UV for the analysis of four drugs in plasma could eliminate interferences from endogenous components of the biological fluids and exhibited sufficient precision and accuracy. These results showed that the prepared Fe₃O₄@FPBA MNPs were qualified for efficiently enriching and determining the trace cis‐diol substances from biological samples. Copyright © 2014 John Wiley & Sons, Ltd.     

Topological identification of the first uninodal 8‐connected lsz MOF built from 2,2′‐difluorobiphenyl‐4,4′‐dicarboxylate pillars and cadmium(II)–triazolate layers

Using polynuclear metal clusters as nodes, many high‐symmetry high‐connectivity nets, like 8‐connnected bcu and 12‐connected fcu , have been attained in metal–organic frameworks (MOFs). However, construction of low‐symmetry high‐connected MOFs with a novel topology still remains a big challenge. For example, a uninodal 8‐connected lsz network, observed in inorganic ZrSiO₄, has not been topologically identified in MOFs. Using 2,2′‐difluorobiphenyl‐4,4′‐dicarboxylic acid (H₂L) as a new linker and 1,2,4‐triazole (Htrz) as a coligand, a novel three‐dimensional Cd^II–MOF, namely poly[tetrakis(μ₄‐2,2′‐difluorobiphenyl‐4,4′‐dicarboxylato‐κ⁵O¹,O^1′:O^1′:O⁴:O^4′)tetrakis(N,N‐dimethylformamide‐κO)tetrakis(μ₃‐1,2,4‐triazolato‐κ³N¹:N²:N⁴)hexacadmium(II)], [Cd₆(C₁₄H₆F₂O₄)₄(C₂H₂N₃)₄(C₃H₇NO)₄]_n, (I), has been prepared. Single‐crystal structure analysis indicates that six different Cd^II ions co‐exist in (I) and each Cd^II ion displays a distorted [CdO₄N₂] octahedral geometry with four equatorial O atoms and two axial N atoms. Three Cd^II ions are connected by four carboxylate groups and four trz⁻ ligands to form a linear trinuclear [Cd₃(COO)₄(trz)₄] cluster, as do the other three Cd^II ions. Two Cd₃ clusters are linked by trz⁻ ligands in a μ_1,2,4‐bridging mode to produce a two‐dimensional Cd^II–triazolate layer with (6,3) topology in the ab plane. These two‐dimensional layers are further pillared by the L²⁻ ligands along the c axis to generate a complicated three‐dimensional framework. Topologically, regarding the Cd₃ cluster as an 8‐connected node, the whole architecture of (I) is a uninodal 8‐connected lsz framework with the Schläfli symbol (4²²·6⁶). Complex (I) was further characterized by elemental analysis, IR spectroscopy, powder X‐ray diffraction, thermogravimetric analysis and a photoluminescence study. MOF (I) has a high thermal and water stability.     

Systematic characterization of the metabolites of echinacoside and acteoside from Cistanche tubulosa in rat plasma,bile, urine and feces based on UPLC‐ESI‐Q‐TOF‐MS

Echinacoside (ECH) and acteoside (ACT), as the most and major active components of Cistanche tubulosa, were reported to possess cardioactive, neuroprotective and hepatocyte protective effects, as well as antibacterial, antioxidative effects. Recently, more studies have focused on their pharmacological activities. However, their metabolic profiles in vivo have not been sufficiently investigated. This study proposes an approach for rapidly identifying the complicated and unpredictable metabolites of ECH and ACT in rat plasma, bile, urine and feces, and systematically and comprehensively revealing their major metabolic pathways, based on powerful ultra‐high performance liquid chromatography coupled with quadrupole time‐of‐flight tandem mass spectrometry. Plasma, bile, urine and feces were collected from rats after a single 200 mg/kg oral dose. A total of 49 metabolites were detected in rat biological samples. Through analyzing metabolites in bile samples, it was found that ECH and ACT were subjected to a marked hepatic first‐pass effect in liver. Copyright © 2016 John Wiley & Sons, Ltd.     

An effective sequence characterized amplified region‐PCR method derived from restriction site‐amplified polymorphism for the identification of female Schistosoma japonicum of zoonotic significance

In the present study, restriction site‐amplified polymorphism (RSAP) markers were used to examine the genetic variability of Schistosoma japonicum isolates from different endemic provinces in mainland China. Of the 45 pairs of primers screened, 10 RSAP markers showed a clear banding pattern with good resolution; however, only six exhibited a polymorphism among different isolates. Among six RSAP markers, one pair of primers (R8+R10) was able to differentiate male and female parasites, and amplified one constant specific band for female S. japonicum isolates. The specific band was recovered, re‐amplified and sequenced, and a sequence of 162 bp was obtained. Based on this sequence, a pair of specific primers was designed and used to develop sequence characterized amplified region (SCAR)‐PCR assay for identification and differentiation of female S. japonicum isolates. The SCAR‐PCR assay allowed the specific identification of female S. japonicum, with no amplicons being amplified from male S. japonicum, Fasciola hepatica, Clonorchis sinensis, S. mansoni (male and female parasite). DNA sequencing confirmed the identity of the amplified products. The minimum amount of DNA detectable using SCAR‐PCR assay was 0.3 ng for female S. japonicum. The SCAR‐PCR was able to differentiate effectively the male and female S. japonicum worms collected from 12 geographical origins in eight endemic provinces, the gender of which was known based on the morphological and biological features. These results showed that SCAR‐PCR provides an effective tool for the sex differentiation studies of S. japonicum, identification of female S. japonicum, diagnosis and epidemiological survey of S. japonicum infections in animals and human.