Detection of agar, by analysis of sugar markers, associated with Bacillus anthracis spores, after culture

Detection of small quantities of agar associated with spores of Bacillus anthracis could provide key information regarding its source or growth characteristics. Agar, widely used in growth of bacteria on solid surfaces, consists primarily of repeating polysaccharide units of 3,6-anhydro-l-galactose (AGal) and galactose (Gal) with sulfated and O-methylated galactoses present as minor constituents. Two variants of the alditol acetate procedure were evaluated for detection of potential agar markers associated with spores. The first method employed a reductive hydrolysis step, to stabilize labile anhydrogalactose, by converting to anhydrogalactitol. The second eliminated the reductive hydrolysis step simplifying the procedure. Anhydrogalactitol, derived from agar, was detected using both derivatization methods followed by gas chromatography-mass spectrometry (GC-MS) analysis. However, challenges with artifactual background (reductive hydrolysis) or marker destruction (hydrolysis) respectively lead to the use of an alternative agar marker. A minor agar component, 6-O-methyl galactose (6-O-M gal), was readily detected in agar-grown but not broth-grown bacteria. Detection was optimized by the use of gas chromatography-tandem mass spectrometry (GC-MS-MS). With appropriate choice of sugar marker and analytical procedure, detection of sugar markers for agar has considerable potential in microbial forensics.     

Application of gas chromatography-mass spectrometry for rapid detection of Mycobacterium xenopi in drinking water.

Gas chromatography-mass spectrometry (GC-MS) was used to detect 2-docosanol, a secondary alcohol characteristic of Mycobacterium xenopi, in 7 of 10 analyzed drinking water samples culture positive for that species. GC-MS was also used to detect tuberculostearic acid. Both of these chemical markers were analyzed as halogenated derivatives in the negative-ion-chemical-ionization mode. The numbers of CFU of M. xenopi were lowest in the three GC-MS-negative samples. The described GC-MS method is useful for the rapid detection of M. xenopi in drinking water.     

Application of gas chromatography-mass spectrometry for rapid detection of Mycobacterium xenopi in drinking water.

Gas chromatography-mass spectrometry (GC-MS) was used to detect 2-docosanol, a secondary alcohol characteristic of Mycobacterium xenopi, in 7 of 10 analyzed drinking water samples culture positive for that species. GC-MS was also used to detect tuberculostearic acid. Both of these chemical markers were analyzed as halogenated derivatives in the negative-ion-chemical-ionization mode. The numbers of CFU of M. xenopi were lowest in the three GC-MS-negative samples. The described GC-MS method is useful for the rapid detection of M. xenopi in drinking water.     

Determination of clenbuterol in human urine by GC-MS-MS-MS: confirmation analysis in antidoping control

This work presents a GC-MS-MS-MS method for the direct determination of clenbuterol in human urine. The method comprises a pretreatment procedure and the instrumental analysis of the derivatives performed by GC-MS(3) (ion trap) with electron impact ionization. The GC-MS(3) analysis allows isolation and characterization of specific fragments from the original (MS(1)) molecular structure, and in particular, those fragments originating from the precursor ion cluster (m/z=335-337) characteristic of clenbuterol. The MS(2) product fragment m/z=300 is in turn used as a further precursor fragment giving rise to a MS(3) spectrum specific for clenbuterol. MS(4) fragmentation spectra were also investigated. However, further fragmentation of MS(3) product ions does not lead to functional MS(4) spectra nor to any significant increase in the signal-to-noise ratio. The sensitivity limit of the MS(3) technique is lower than 0.2 microg/l, with a linear range between 0.5 and 5 microg/l, thus matching the basic requirements for antidoping analysis according to the guidelines of the International Olympic Committee. Due to its overall analytical performance, the method is presently being evaluated as a confirmation protocol to be followed to detect illicit clenbuterol administration to the athletes, and compared with reference GC-MS and GC-MS-MS techniques.     

Improved methodology for the detection and quantitation of urinary metabolites of sulphur mustard using gas chromatography-tandem mass spectrometry

Gas chromatography-tandem mass spectrometry (GC-MS-MS) with selected-reaction monitoring was applied to the analysis of urinary metabolites of sulphur mustard, derived from the β-lyase pathway and from hydrolysis. In the case of β-lyase metabolites, a limit of detection of 0.1 ng/ml was obtained, compared to 2–5 ng/ml using single stage GC-MS with selected-ion monitoring. GC-MS-MS methodology was less useful when applied to the analysis of thiodiglycol bis(pentafluorobenzoate) using negative-ion chemical ionisation although selected-reaction chromatograms were cleaner than selected-ion chromatograms. The advantage of using GC-MS-MS was demonstrated by the detection of low levels of β-lyase metabolites in the urine of casualties who had been exposed to sulphur mustard.     

An exometabolomics approach to monitoring microbial contamination in microalgal fermentation processes by using metabolic footprint analysis

The early detection of microbial contamination is crucial to avoid process failure and costly delays in fermentation industries. However, traditional detection methods such as plate counting and microscopy are labor-intensive, insensitive, and time-consuming. Modern techniques that can detect microbial contamination rapidly and cost-effectively are therefore sought. In the present study, we propose gas chromatography-mass spectrometry (GC-MS)-based metabolic footprint analysis as a rapid and reliable method for the detection of microbial contamination in fermentation processes. Our metabolic footprint analysis detected statistically significant differences in metabolite profiles of axenic and contaminated batch cultures of microalgae as early as 3 h after contamination was introduced, while classical detection methods could detect contamination only after 24 h. The data were analyzed by discriminant function analysis and were validated by leave-one-out cross-validation. We obtained a 97% success rate in correctly classifying samples coming from contaminated or axenic cultures. Therefore, metabolic footprint analysis combined with discriminant function analysis presents a rapid and cost-effective approach to monitor microbial contamination in industrial fermentation processes.     

Rapid identification of microbial VOCs from tobacco molds using closed-loop stripping and gas chromatography/time-of-flight mass spectrometry

Several microbial volatile organic compounds (MVOCs) that can serve as potential chemical markers for microbial contamination in tobacco have been identified. Four different fungal species, Aspergillus niger (AN), A. ornatus (AO), Pencillium chrysogenum (PC) and Rhizopus stolonifer (RS), commonly reported in moldy tobacco were cultured and screened for MVOCs. Because the MVOCs emitted by a microbial species are substrate specific, the fungal strains were separately grown on potato dextrose agar (PDA) and tobacco products. MVOCs from the mold cultures grown on PDA and tobacco products were extracted using closed-loop stripping analysis (CLSA) and identified by gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS). Some of the prominent tobacco mold markers identified by this method include: 1-octen-3-ol; 2-octen-1-ol; 2-methyl-1-butanol; 3-methyl-1-butanol; 1-octene and 2-pentanone. In particular, 1-octen-3-ol was detected in all the mold cultures and moldy tobacco samples analyzed. Olfactory evaluation of 1-octen-3-ol indicated a characteristic musty odor and the odor threshold was determined to be approximately 200 ng/ml. The limits of detection for 1-octen-3-ol using GC/TOF-MS and GC/mass selective detector (MSD) in the full-scan mode and selected ion monitoring (SIM) mode were investigated. The CLSA-GC/TOF-MS demonstrates a fast, sensitive and semi-quantitative analytical technique for screening tobacco materials for the presence of mold via chemical markers of microbial contamination.     

Identification of bacterial DNA markers for the detection of human fecal pollution in water

We used genome fragment enrichment and bioinformatics to identify several microbial DNA sequences with high potential for use as markers in PCR assays for detection of human fecal contamination in water. Following competitive solution-phase hybridization of total DNA from human and pig fecal samples, 351 plasmid clones were sequenced and were determined to define 289 different genomic DNA regions. These putative human-specific fecal bacterial DNA sequences were then analyzed by dot blot hybridization, which confirmed that 98% were present in the source human fecal microbial community and absent from the original pig fecal DNA extract. Comparative sequence analyses of these sequences suggested that a large number (43.5%) were predicted to encode bacterial secreted or surface-associated proteins. Deoxyoligonucleotide primers capable of annealing to a subset of 26 of the candidate sequences predicted to encode factors involved in interactions with host cells were then used in the PCR and did not amplify markers in DNA from any additional pig fecal specimens. These 26 PCR assays exhibited a range of specificity in tests with 11 other animal sources, with more than half amplifying markers only in specimens from dogs or cats. Four assays were more specific, detecting markers only in specimens from humans, including those from 18 different human populations examined. We then demonstrated the potential utility of these assays by using them to detect human fecal contamination in several impacted watersheds.     

Blood gene expression markers to detect and distinguish target organ toxicity

The purpose of this study was to investigate whether the expression of specific genes in peripheral blood can be used as surrogate marker(s) to detect and distinguish target organ toxicity induced by chemicals in rats. Rats were intraperitoneally administered a single, acute dose of a well-established hepatotoxic (acetaminophen) or a neurotoxic (methyl parathion) chemical. Administration of acetaminophen (AP) in the rats resulted in hepatotoxicity as evidenced from elevated blood transaminase activities. Similarly, administration of methyl parathion (MP) resulted in neurotoxicity in the rats as evidenced from the inhibition of acetyl cholinesterase activity in their blood. Administration of either chemical also resulted in mild hematotoxicity in the rats. Microarray analysis of the global gene expression profile of rat blood identified distinct gene expression markers capable of detecting and distinguishing hepatotoxicity and neurotoxicity induced by AP and MP, respectively. Differential expressions of the marker genes for hepatotoxicity and neurotoxicity were detectable in the blood earlier than the appearance of the commonly used clinical markers (serum transaminases and acetyl cholinesterase). The ability of the marker genes to detect hepatotoxicity and neurotoxicity was further confirmed using the blood samples of rats administered additional hepatotoxic (thioacetamide, dimethylnitrobenzene, and carbon tetrachloride) or neurotoxic (ethyl parathion and malathion) chemicals. In summary, our results demonstrated that blood gene expression markers can detect and distinguish target organ toxicity non-invasively.     

Identification of Bacterial DNA Markers for the Detection of Human Fecal Pollution in Water

We used genome fragment enrichment and bioinformatics to identify several microbial DNA sequences with high potential for use as markers in PCR assays for detection of human fecal contamination in water. Following competitive solution-phase hybridization of total DNA from human and pig fecal samples, 351 plasmid clones were sequenced and were determined to define 289 different genomic DNA regions. These putative human-specific fecal bacterial DNA sequences were then analyzed by dot blot hybridization, which confirmed that 98% were present in the source human fecal microbial community and absent from the original pig fecal DNA extract. Comparative sequence analyses of these sequences suggested that a large number (43.5%) were predicted to encode bacterial secreted or surface-associated proteins. Deoxyoligonucleotide primers capable of annealing to a subset of 26 of the candidate sequences predicted to encode factors involved in interactions with host cells were then used in the PCR and did not amplify markers in DNA from any additional pig fecal specimens. These 26 PCR assays exhibited a range of specificity in tests with 11 other animal sources, with more than half amplifying markers only in specimens from dogs or cats. Four assays were more specific, detecting markers only in specimens from humans, including those from 18 different human populations examined. We then demonstrated the potential utility of these assays by using them to detect human fecal contamination in several impacted watersheds.     

Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems

PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.     

Separation and confirmation of anabolic steroids with quadrupole ion trap tandem mass spectrometry

Gas chromatography-mass spectrometry (GC-MS) is the method of choice for separation and detection of anabolic steroids in urine. Recently, there have been advances in the areas of gas chromatography columns, tandem mass spectrometry using ion traps, and large volume sample injection that have promise for lowering detection limits and extending the utility of GC-MS for steroid analysis. In this work, a Varian Saturn III GC-MS system has been used in its tandem mass spectrometry mode to detect low picogram levels of model steroids in standard solution and the urine matrix. Application of MS-MS-MS provided structurally informative spectra for 3′-hydroxystanozolol at concentrations of 1 ng/ml. In addition, four polysilphenylene-polydimethylsiloxane capillary columns were examined for background and selectivity. The columns had bleed several-fold lower than conventional polysiloxane columns. The columns also exhibited significant differences in selectivity for structurally similar steroids. Finally, a new temperature-programmed split-splitless injector was used to inject as much as 25 μl on column. The resulting limits of detection were 5 pg/ml for norandrosterone.     

Detection of cocaine and cocaethylene in sweat by solid-phase microextraction and gas chromatography/mass spectrometry

In the present work, a semi-quantitative method was developed to detect simultaneously cocaine (COC) and cocaethylene (CE) (transesterification product of the coingestion of COC with ethanol) in sweat. Sweat samples were collected by means of a non-occlusive sweat patch device supplied by PharmChek. The method was based on the dissolution of COC and CE incorporated into the patch, with 0.2 M sodium acetate buffer (pH 5.0) and the extraction of the analytes by solid-phase microextraction (SPME). Gas chromatography/mass spectrometry (GC-MS) was used to detect the analytes in selected ion monitoring mode (SIM). The method showed to be very simple, rapid and sensitive. The limits of detection were 5 ng/ml for COC and CE (12.5 ng/patch). Good inter and intra-assay precision was also observed (coefficient of variation <8%) with the use of deuterated internal standards.     

Application of capillary gas chromatography-mass spectrometry to chemical characterization of radiation-induced base damage of DNA: implications for assessing DNA repair processes

The application of capillary gas chromatography-mass spectrometry (GC-MS) to the chemical characterization of radiation-induced base products of calf thymus DNA is presented. Samples of calf thymus DNA irradiated in N2O-saturated aqueous solution were hydrolyzed with HCOOH, trimethylsilylated, and subjected to GC-MS analysis using a fused-silica capillary column. Hydrolysis conditions suitable for the simultaneous analysis of the radiation-induced products of all four DNA bases in a single run were determined. The trimethylsilyl derivatives of these products had excellent GC properties and easily interpretable mass spectra; an intense molecular ion (M+.) and a characteristic (M-CH3)+ ion were observed. The complementary use of t-butyldimethylsilyl derivatives was also demonstrated. These derivatives provided an intense characteristic (M-57)+ ion, which appeared as either the base peak or the second most intense ion in the spectra. All mass spectra obtained are discussed. Because of the excellent resolving power of capillary GC and the accurate high-sensitivity identification by MS, the capillary GC-MS is suggested as a very suitable technique for identification of altered bases removed from DNA by base excision-repair enzymes such as DNA glycosylases and, thus, as very useful for an understanding of the base excision-repair of DNA.     

The Detection of Microorganisms and Organic Material on Stainless Steel Food Contact Surfaces

Few methods are available for the differentiation of microorganism and organic material on surfaces, although such mixtures are commonplace, particularly in the food industry, where food debris (soil) and microorganisms frequently foul food contact surfaces and pose challenges in terms of hygiene and cleanability. It would be of value to discern any differences in removal or persistence on surfaces. This review considers some methods which are available. Direct epifluorescence microscopy (DEM) enables visual differentiation, but traditional microbiological culture methods cannot detect organic soil. Atomic force microscopy (AFM) provides images of the surface on the nanometer scale, with minimal preparation, and is able to visualise both cellular and acellular components of the mixture, particularly prior to cleaning. Confocal laser scanning microscopy (CLSM) also has potential in this area. Surface sensitive methods such as X-Ray photoelectron spectroscopy (XPS) and Time-of-flight secondary ion mass spectrometry (ToFSIMS) provide information on chemical species present on a surface. Those chemical species more likely on microbial cells may be differentiated from those more likely in a specified organic soil, thus comparisons may be made as to differential removal of the organic soil and microbial cells. These methods may be of value in studies on the fouling and cleanability of surfaces.     

HS-SPME-GC/MS法分析中缅树鼩尿液的化学成分

正尿液是动物新陈代谢的产物,在动物的化学通讯中发挥着重要作用,动物依靠它识别个体,选择高质量的配偶,判断亲缘关系,吸引异性等,以增加个体的适合度(Macdonald and Brown,1985)。各种动物尿液的化学成分复杂,含有挥发性和非挥发性两类化学信号物质。尿液的化学组成和其功能在许多动物中已进行报道,如大熊猫(Ailuropoda melanoleuca)(刘玉良等,2012)、水獭(Arvicola     

Identification of mycotoxins in keratomycosis-derived Fusarium isolates by gas chromatography—mass spectrometry

The production of mycotoxins from Fusarium species has been demonstrated in isolates cultured from patients suffering from keratomycosis. The method employed a combination of thin-layer chromatography directly performed on gel plugs taken from the growth medium, cartridge column chromatography, silylation and gas chromatography on a non-polar stationary phase capillary column linked to mass spectrometry. The sensitivities of detection obtained for a signal-to-noise ratio of 33:1, were 200 pg for single stage GC-MS and 20 pg using tandem GC-MS-MS. Two mycotoxins, diacetoxyscirpenol and T-2 toxin were identified in three cultures.     

High sensitivity negative ion GC-MS method for detection of desaturated and chain-elongated products of deuterated linoleic and linolenic acids.

A sensitive negative chemical ionization (NCI) gas chromatography-mass spectrometry (GC-MS) method for the detection of pentafluorobenzyl (PFB) esters of deuterated fatty acids is described. Deuterated linoleic [18:2n-6 2H4-9,10,12,13] and linolenic [18:3n-3 2H5-17,17,18,18,18] acids were converted to chain-elongated and desaturated products during incubations with homogenates prepared from rat liver. The extracted fatty acids were derivatized with pentafluorobenzyl bromide and analyzed in the negative ion mode by GC-MS. The detection limit of the PFB esters in NCI using selected ion monitoring was below 10 femtograms. In general, detection of the PFB derivatives using the negative ion mode was more than three orders of magnitude more sensitive than using a positive chemical ionization (PCI) method with methyl ester derivatives. The PFB esters of the 2H4-18:2n-6 metabolites eluted with their unlabeled analogues, whereas the PFB esters of the 2H5-18:3n-3 metabolites were resolved from the unlabeled compounds on polar capillary FFAP columns. Isotope ratios of the 2H4-18:2n-6 metabolites were used to quantify the deuterated compounds from standard dilution curves generated from the ion abundances of the unlabeled fatty acids. The 2H5-18:3n-3 metabolites were quantified similarly using 18:3n-3. This method is feasible for the study of the in vivo metabolism of deuterated essential fatty acids in whole animals.     

Determination of cocaine, benzoylecgonine and cocaethylene in human hair by solid-phase microextraction and gas chromatography-mass spectrometry

The present work describes a highly precise and sensitive method developed to detect cocaine (COC), benzoylecgonine (BE, its main metabolite) and cocaethylene (CE, transesterification product of the coingestion of COC with ethanol) in human head hair samples. The method was based on an alkylchloroformate derivatization of benzoylecgonine and the extraction of the analytes by solid-phase microextraction (SPME). Gas chromatography-mass spectrometry (GC-MS) was used to identify and quantify the analytes in selected ion monitoring mode (SIM). The limits of quantification and detection (LOQ and LOD) were: 0.1 ng/mg for COC and CE, and 0.5 ng/mg for BE. Good inter- and intra-assay precision was observed. The dynamic range of the assay was 0.1-50 ng/mg. The method is not time consuming and was shown to be easy to perform.     

Limits of detection for the determination of mono- and dicarboxylic acids using gas and liquid chromatographic methods coupled with mass spectrometry

The chromatographic separation and instrumental limits of detection (LODs) were obtained for a broad range of C(1)-C(18) monocarboxylic (MCAs) and C(2)-C(14) dicarboxylic acids (DCAs) employing either chemical derivatization followed by gas chromatography-mass spectrometry and flame ionization detection (GC-MS/FID) or direct analysis with liquid chromatography high resolution MS and tandem MS (LC-MS). Suitability, efficiency and stability of reaction products for several derivatization agents used for esterification (BF(3)/butanol), and trimethysilylation, including trimethylsilyl-N-N-dimethylcarbamate (TMSDMC) and N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) were evaluated. The lowest limits of detection for the majority of compounds below 10 pg (with the exception of acetic acid) were obtained for derivatization with BF(3)/butanol followed by GC-MS in the total ion current (TIC) mode. Further improvements were achieved when applying either selected ion monitoring (SIM), which decreased the LODs to 1-4 pg or a combination of SIM and TIC (SITI) (2-5 pg). GC-FID provided LODs comparable to those obtained by GC-MS TIC. Both trimethylsilylation (followed by GC-MS) and direct LC-MS/MS analysis yielded LODs of 5-40 pg for most of the acids. For volatile acids the LODs were higher, e.g., 25 and 590 ng for TMSDMC and BSTFA derivatized formic acid, respectively, whereas the LC-MS methods did not allow for the analysis of formic acid at all.