Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

Species identification of fragmentary bone, such as in rendered meat and bone meal or from archaeological sites, is often difficult in the absence of clear morphological markers. Here we present a robust method of analysing genus-specific collagen peptides by mass spectrometry simply by using solid-phase extraction (a C18 ZipTip) for peptide purification, rather than liquid chromatography/mass spectrometry (LC/MS). Analysis of the collagen from 32 different mammal species identified a total of 92 peptide markers that could be used for species identification, for example, in processed food and animal feed. A set of ancient (>100 ka@10 degrees C) bone samples was also analysed to show that the proposed method has applications to archaeological bone identification.

Determination of halogenated natural products in passive samplers deployed along the Great Barrier Reef, Queensland/Australia

Halogenated natural products (HNPs) have been increasingly reported to occur in marine wild life from all oceans. Several HNPs, such as 2,3,3',4,4',5,5'-heptachloro-1'-methyl-1,2'-bipyrrole (1) and 4,6-dibromo-2-(2',4'-dibromo)phenoxyanisole (2'-MeO-BDE 68 or BC-2), were detected at particularly high concentrations in dolphins from Queensland/Australia. About half of the coastline of Queensland (approximately 2500 km) is covered by the Great Barrier Reef, a rich ecosystem hosting a huge variety of species, many of which are known to produce natural compounds. In this study, semipermeable membrane devices (SPMDs) were deployed as passive samplers for about 30 days at 12 marine and 2 nonmarine sites (i.e., rivers) along the Great Barrier Reef as part of a routine monitoring program during November 2007 and May 2008. Q1 and 2'-MeO-BDE 68 were detected at the marine sites with frequencies of about 65% but not in any sample from the two rivers. Further HNPs (2,4,6-tribromophenol, TBP; 2,4,6-tribromoanisole, TBA; 2,2'-dimethoxy-3,3'5,5'-tetrabromobiphenyl, 2,2'-diMeO-BB 80 or BC-1; 3,5-dibromo-2-(2',4'-dibromo)phenoxyanisole, 6-MeO-BDE 47 or BC-3; and 3,5-dibromo-2-(3',5'-dibromo,2'-methoxy)phenoxyanisole, 2',6-diMeO-BDE 68 or BC-11) were detected as well with frequencies of 18-97% in the marine samples, but no polybrominated flame retardants were detected. The highest amount of a single HNP, 2.3 microg/SPMD, was determined for TBP, which had a frequency of detection of only 46%. The maximum (average) amount in the SPMDs from marine sites was 44 ng (12 ng) for (1 and 115 ng (20 ng) for 2'-MeO-BDE 68. A first order kinetic model was used to estimate concentrations of the HNPs in the water phase. Based on the depuration of performance reference compounds obtained at one of the sites, we assumed a sampling rate of 16 L/day. We used this sampling rate to estimate that the highest and average available concentrations of Q1 in the water during the deployment of the SPMD were 97 and 25 pg/L, respectively. The estimated maximum water concentrations of 2'-MeO-BDE 68, 2,2'-diMeO-BB 80, 6-MeO-BDE 47, and 2',6-diMeO-BDE 68 were on average 2-5.5 fold higher than that of Q1. The results confirm that the HNPs are produced throughout the Great Barrier Reef, which appears to be a significant source of these compounds.

Analysis of biopharmaceutical market-appropriate plastic syringe barrel for extractables

A study was designed to evaluate a new syringe system developed specifically for sensitive pharmaceutical and biopharmaceutical drug products. An in-depth review of the extractables portion of this program is presented and includes data generated by liquid chromatography-mass spectroscopy, gas chromatography-mass spectroscopy, ion chromatography, and inductively coupled plasma of the Crystal Zenith barrel before and after sterilization. One leachable was identified after e-beam irradiation processing. This leachable, identified as an organic acid species, was then evaluated from a safety assessment viewpoint. The details of this program and associated results are explained in this report.

NMR quantitation of natural products at the nanomole scale

We describe a simple and accurate method for quantitation by solvent 13C-satellites (QSCS) of very small amounts of natural products using microprobe NMR spectroscopy. The method takes advantage of integration of 13C satellite peaks of deuterated solvents, in particular CDCl3, that have favorable intensities for measurements of samples in NMR microcoils and microprobe tubes in the 1-200 nanomole range.

Risk reduction in biotherapeutic products

Ensuring the safety of therapeutic modalities produced and purified from biological systems is of high concern. Regulatory authorities and the biopharmaceutical industry are continuously seeking to improve methods for the detection, identification, inactivation and removal of potentially contaminating pathogens in biotherapeutic products. Current methods for pathogen detection and identification are designed to discover adventitious as well as known microbial species in product samples. Many of these approaches require weeks or even months of observation, and the time involved is often a constraint on product release. This review focuses on current practices and technologies that have emerged in recent years, and highlights advances that have accelerated the time required for, and accuracy of, pathogen detection and identification. The biopharmaceutical industry has employed a multifaceted approach in pathogen detection, including the rigorous screening of blood/plasma donations; documented sourcing and screening of raw materials; thorough testing of production cell substrates and cell culture harvest material during processing, and at the stage of a final purified drug substance; and the evaluation of microbe clearance during purification operations. All these practices strive to ensure safety and mitigate the risk to patients undergoing biotherapeutic treatment.

Solvent derived artifacts in natural products chemistry

Solvents play an important and critical role in natural product chemistry. They are mainly used during the extraction and purification of metabolites from a biological matrix. To a lesser extent, solvents are also used as reagents or catalysts to perform chemical reactions. This review focuses on the most important classes of solvents, including alcohols, halogen-containing solvents, esters, ethers, acids and bases. The chemical reactions associated with the use of these solvents to form the so-called "artifacts" are discussed and the most common contaminants found in these solvents are also reviewed. The formation of artifacts and the use of contaminated solvents mainly leads to the formation of new compounds, loss of activity of active compounds, formation of active compounds from inactive ones (false positives), loss in total yield of important compounds during isolation, formation of toxic compounds and difficulty in reproducing an extraction or purification method. Finally, the need for stability studies of purified natural products is emphasized, as this is a common overlooked aspect in natural product chemistry.

Contrasting the seasonal variability of halogenated natural products and anthropogenic hexachlorocyclohexanes in the southern Norwegian atmosphere

Halogenated natural products (HNPs) are increasingly recognized as compounds of marine environmental samples. In this study, we explored whether the annual course of the concentrations of HNPs in ambient air samples was different from those of anthropogenic pollutants. For this purpose, air samples taken weekly at Lista, southern Norway, were analyzed by gas chromatography-mass spectrometry for anthropogenic aaeeee- (alpha-HCH) and aaaeee-hexachlorocyclohexane (gamma-HCH, lindane) isomers, as well as the HNPs 2,3,3',4,4',5,5'-heptachloro-1'-methyl-1,2'-bipyrrole (Q1), 2,4-di- and 2,4,6-tribromoanisole (24-DBA, 246-TBA), and 2,4,6-tribromophenol (246-TBP). Concentrations of HCH isomers were higher in the warmer summer months than in winter. By contrast, Q1, 24-DBA, 246-TBA, and 246-TBP showed much higher concentrations at the end of the year. Correlations between the concentrations of the compounds and air mass trajectories as well as further meteorological data are discussed. An unknown mixed halogenated substance was detected at high abundance during the summer months. High-resolution mass spectrometry and tandem mass spectrometric techniques were used to unravel the molecular structure, which was found to be C(7)H(8)Br(3)Cl, an elemental composition never reported before in the scientific literature.

Purity-activity relationships of natural products: the case of anti-TB active ursolic acid

The present study explores the variability of biological responses from the perspective of sample purity and introduces the concept of purity-activity relationships (PARs) in natural product research. The abundant plant triterpene ursolic acid (1) was selected as an exemplary natural product due to the overwhelming number yet inconsistent nature of its approximate 120 reported biological activities, which include anti-TB potential. Nine different samples of ursolic acid with purity certifications were obtained, and their purity was independently assessed by means of quantitative 1H NMR (qHNMR). Biological evaluation consisted of determining MICs against two strains of virulent Mycobacterium tuberculosis and IC50 values in Vero cells. Ab initio structure elucidation provided unequivocal structural confirmation and included an extensive 1H NMR spin system analysis, determination of nearly all J couplings and the complete NOE pattern, and led to the revision of earlier reports. As a net result, a sigmoid PAR profile of 1 was obtained, demonstrating the inverse correlation of purity and anti-TB bioactivity. The results imply that synergistic effects of 1 and its varying impurities are the likely cause of previously reported antimycobacterial potential. Generating PARs is a powerful extension of the routinely performed quantitative correlation of structure and activity ([Q]SAR). Advanced by the use of primary analytical methods such as qHNMR, PARs enable the elucidation of cases like 1 when increasing purity voids biological activity. This underlines the potential of PARs as a tool in drug discovery and synergy research and accentuates the need to routinely combine biological testing with purity assessment.

[Viral safety of biologicals]

The viral safety of biologicals, either human blood derivatives or animal products or recombinant proteins issued from biotechnology, relies on the quality of the starting material, the manufacturing process and, if necessary, the control of the final product. The quality of the starting material is highly guaranteed for blood derivatives due to the individual screening for specific markers (antigens, genome, antibodies) for major blood borne viruses such as hepatitis B and C viruses (HBV, HCV) and human immunodeficiency virus (HIV). It can be reinforced by the detection through amplification procedures (polymerase chain reaction) in the plasma pool of genomes from viruses that have been implicated in contaminations of blood derivatives in the past (parvovirus B19, hepatitis A virus). The association in the manufacturing process of different steps dedicated to purification of plasma proteins (partitioning), virus inactivation (solvent/detergent treatment, heat inactivation) or specific procedures allowing virus removal (nanofiltration) allows to reduce the viral risk very efficiently. The validation studies using scaled down systems and model viruses allow to evaluate the virus safety of any product quantitatively. The aim of these procedures is to guarantee the lack of infectivity due to any virus, either known or unknown.

[NIRS method for determination of meat and bone meal content in ruminant concentrates]

Feed contaminated with MBM is commonly accepted as the main transmission carrier of bovine spongiform encephalopathy (BSE). To prevent BSE many countries have banned MBM as a feed ingredient. In the People's Republic of China, the ban was first applied to ruminant feed. In order to investigate the feasibility of near infrared diffuse reflectance spectroscopy method for rapidly quantitative determination of meat and bone meal content in ruminant concentrates, 225 representatively commercial ruminant concentrates samples and 75 meat and bone meal (including cattle, sheep, pig and poultry meat and bone meal) samples were collected in the People's Republic of China. Two hundred twenty five ruminant concentrates samples of adulterated meat and bone meal (0.5%-35%) were prepared including 135 calibration samples and 90 independent validation samples. For the calibration set samples, 3 samples were prepared at each concentration. For validation set samples, 2 samples were prepared at each concentration. Any one commercial ruminant concentrates was used once only. The spectra were scanned by raster near infrared diffuse reflectance spectroscopy instrument, and the effect of spectrum pretreatment methods (mathematic pretreatments and scatter correction) and spectrum region (visible and NIR) on the calibration results was considered. The calibration equation was established by modified partial least squares method. The result showed that the calibration gave r2 of 0.979, a standard error of calibration (SEC) of 1.522% and a standard error of cross validation (SECV) of 1.582%. The 90 independent validation samples were used to validate the quantitative equation. The r2, a standard error of prediction (SEP) and ratio of performance to standard deviation (RPD) were 0.972, 1.764% and 5.99 respectively. The results of this study indicated that near infrared diffuse reflectance spectroscopy method could provide rapidly quantitative prediction for meat and bone meal percent in ruminant concentrates. This method was significant in practice for enriching the rapidly quantitative methods of determining animal feed materials.

Determination of analyte concentration using the residual solvent resonance in (1)H NMR spectroscopy

An NMR protocol that uses the residual proton signal from DMSO -d(6) (i.e., DMSO -d(5)) to determine the concentration of an analyte in a NMR sample was developed. This technique provides an alternative method for determining the molar concentration of compounds in solution without prior knowledge of their molecular weight. The method is particularly useful when submilligram quantities of compound are to be analyzed and is applicable to a variety of different research areas such as compound management, and natural product, combinatorial, and medicinal chemistry.

Combining HPLC-PDA-MS-SPE-NMR with circular dichroism for complete natural product characterization in crude extracts: levorotatory gossypol in Thespesia danis

Despite recent demonstration of the power of HPLC-PDA-MS-SPE-NMR (high-performance liquid chromatography-photodiode-array detection-mass spectrometry-solid-phase extraction-nuclear magnetic resonance) in structure determination of natural products directly from minute amounts of crude extracts, this technique leaves chirality of the compounds uncharacterized. In this work we demonstrate that postcolumn SPE is a useful method of analyte concentration and accumulation not only for NMR but also for CD (circular dichroism) spectroscopy. Thus, use of HPLC-PDA-MS-SPE-NMR in combination with CD allowed rapid detection of ( R)-(-)-gossypol [( R)- 1] in Thespesia danis, providing a very rare example of the predominance of the levorotatory enantiomer of gossypol. Enantioselectivity of the in vitro antiplasmodial activity of gossypol was also demonstrated; the IC50 value of ( R)- 1 was 4.5 +/- 0.2 microM, with the eudismic ratio of about 2.5. No gossypol was detected in Gossypioides kirkii.

[Discriminant analysis of near infrared diffuse reflectance spectra to detect adulteration of non-ruminant meat and bone meal]

In order to study the feasibility of using near infrared (NIR) diffuse reflectance spectroscopy to discriminate adultera tion of non-ruminant meat and bone meal (MBM) with ruminant MBM, a total of 39 MBM samples made up of 15 from pig, 15 from poultry, 5 from cattle and 4 from sheep produced in different areas in China were chosen. The MBM samples were ground with 0. 5 mm sieve. 252 specimens were prepared by non-ruminant MBM deliberately adulterated with different proportion of ruminant MBM. The specimens were scanned by FOSS NIRSystem 6500. A calibration set of 180 specimens and an independent validation set of 72 specimens were randomly selected by the WINISI software. Discriminant analysis model was developed by partial least squares (PLS) on the calibration set and validated with independent validation set. The best discriminant model was obtained using standard normal variate and detrend (SNVD) and second derivative for spectrum pretreatment; this model had a coefficient of determination (R2(CV)) of 0.83 and a standard error of cross-validation (SECV) of 0. 147 1. For the independent validation set, the correct classification rate is 90%. There were a false negative specimen (0.5%) and two uncertain specimens (1%, 1.5%) in validation set. Results showed that it is feasible to use NIR diffuse reflectance spectroscopy to discriminate adulteration of non-ruminant MBM with ruminant MBM, but for specimens adulterated with ruminant MBM at less than 2%, the accuracy of calibration model needs to be improved. NIR was a rapid and non-destructive approach to discriminating adulteration of non-ruminant MBM with ruminant MIBM.

WHO Study Group on cell substrates for production of biologicals, Geneva, Switzerland, 11-12 June 2007

For many years, the World Health Organization (WHO) has provided global leadership in defining technical specifications for quality assurance and safety of biological medicines produced in cell substrates. Current WHO requirements for the use of animal cells as substrates for production of vaccines and other biologicals were adopted by the WHO Expert Committee on Biological Standardization in 1996 (WHO TRS 878). Since then, significant progress especially in the development of vaccines in novel continuous cell lines of mammalian origin as well as in insect cells has been made and consequently there is an increasing need for the re-evaluation of existing criteria for the acceptability of such cell lines. In addition there is also a need to consider new issues in cell substrate safety arising from these new cell types and developments in technology and scientific knowledge. In response to these demands, the WHO Study Group on Cell Substrates was formed in 2006 to initiate revision of WHO requirements and to address the need for further research in this area. At its second meeting on 11-12 June 2007, the Study Group reviewed scientific data that would form the basis for new recommendations and made a number of proposals for further investigations. The Study Group is working on the preparation of a revised WHO document, and a broad consultation with regulators, manufacturers, and other relevant parties is planned for 2008.

Differentiation of wastewater effluent organic matter (EfOM) from natural organic matter (NOM) using multiple analytical techniques

Using three analytical techniques of size exclusion chromatography (SEC), fluorescence excitation-emission matrix (EEM), and dissolved organic nitrogen (DON) measurement, differentiating characteristics of effluent organic matter (EfOM) from natural organic matter (NOM) have been investigated. SEC reveals a wide range of molecular weight (MW) for EfOM and high amount of high MW polysaccharides, and low MW organic acids compared to NOM. Clear protein-like peaks using fluorescence EEM were a major feature of EfOM distinguishing it from NOM. Fluorescence index (FI), an indicator to distinguish autochthonous origin from allochthonous origin, differentiated EfOM from NOM by exhibiting higher values, indicating a microbial origin. In EfOM samples, DON present in higher amounts than NOM.

Weighing of biomolecules, single cells and single nanoparticles in fluid

Nanomechanical resonators enable the measurement of mass with extraordinary sensitivity. Previously, samples as light as 7 zeptograms (1 zg = 10(-21) g) have been weighed in vacuum, and proton-level resolution seems to be within reach. Resolving small mass changes requires the resonator to be light and to ring at a very pure tone-that is, with a high quality factor. In solution, viscosity severely degrades both of these characteristics, thus preventing many applications in nanotechnology and the life sciences where fluid is required. Although the resonant structure can be designed to minimize viscous loss, resolution is still substantially degraded when compared to measurements made in air or vacuum. An entirely different approach eliminates viscous damping by placing the solution inside a hollow resonator that is surrounded by vacuum. Here we demonstrate that suspended microchannel resonators can weigh single nanoparticles, single bacterial cells and sub-monolayers of adsorbed proteins in water with sub-femtogram resolution (1 Hz bandwidth). Central to these results is our observation that viscous loss due to the fluid is negligible compared to the intrinsic damping of our silicon crystal resonator. The combination of the low resonator mass (100 ng) and high quality factor (15,000) enables an improvement in mass resolution of six orders of magnitude over a high-end commercial quartz crystal microbalance. This gives access to intriguing applications, such as mass-based flow cytometry, the direct detection of pathogens, or the non-optical sizing and mass density measurement of colloidal particles.

The application of electrospray ionization coupled to ultrahigh resolution mass spectrometry for the molecular characterization of natural organic matter

Mass spectrometry has recently played a key role in the understanding of natural organic matter (NOM) by providing molecular-level details about its composition. NOM, a complex assemblage of organic molecules present in natural waters and soils/sediments, has the ability to bind and transport anthropogenic materials. An improved understanding of its composition is crucial in order to understand how pollutants interact with NOM and how NOM cycles through global carbon cycles. In the past, low-resolution (>3000) mass analyzers have offered some insights into the structure of NOM, but emerging ultrahigh resolution (>200,000) techniques such as electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) have significantly advanced our knowledge of NOM chemistry. Here, a review of the recent literature on the advancements of NOM characterization and the applications of mass spectrometry to this central task is presented. Various methods for the analysis and display of the extremely complex mass spectra, such as the van Krevelen diagram and Kendrick mass defect analysis, are discussed. We also review tandem mass spectrometry techniques employed to gain structural information about NOM components. Finally, we show how ESI-FT-ICR-MS has been applied to examine specific issues that are important to the NOM scientific community, such as NOM reactivity, transport and fate, degradation, and existence of components, which are indicators of NOM origin. In general, ultrahigh resolution provided by FT-ICR-MS is essential for the complete separation of the thousands of peaks present in the complex NOM mixture and will clearly lead to additional future advancements in the areas of aquatic, soil, and analytical chemistry.

Case-control study on feed risk factors for BSE cases born after the feed ban in France

In France, after the ban on meat and bone meal (MBM) in cattle feeding in June 1990, cases of Bovine Spongiform Encephalopathy (BSE) have continued to be detected in bovines born after that ban (called BAB cases). A case-control study was therefore carried out to determine the way these cases were contaminated. A multivariate conditional model was built adjusting for the production type of the animals and taking into account the herd size. The results confirmed that feeding cattle with proprietary concentrates was at risk for BSE, with an adjusted odds ratio of 6.8 (2.5; 18.7) for the consumption of less or three different proprietary concentrates and 17.6 (5.7; 54.8) for more than three, when comparing with no consumption of proprietary concentrates, considering feeding of bovines before the age of two. The results suggest that cross-contaminations by MBM in bovine concentrates have occurred after 1990. To a lesser extent, on-farm cross-contaminations, i.e. consumption by cattle of feedstuffs initially dedicated to other animals and which could legally contain MBM, have probably also existed, since the presence on farms of poultry fed purchased feed involved an increased risk of BSE with an odds ratio of 1.8 (1.1; 3.0). The use of milk replacers, which often incorporates animal fats, was also at risk with an odds ratio of 1.8 (1.0; 3.1).

Identification of natural products using HPLC-SPE combined with CapNMR

Two major development areas in HPLC-NMR hyphenation are postcolumn solid-phase extraction (HPLC-SPE-NMR) and capillary separations with NMR detection by means of solenoidal microcoils (CapNMR). These two techniques were combined off-line into HPLC-SPE-CapNMR, which combines the advantage of high loadability of normal-bore HPLC columns with high mass sensitivity of capillary NMR probes with an active volume of 1.5 microL. The technique was used for rapid identification of complex sesquiterpene lactones and esterified phenylpropanoids present in an essentially crude plant extract (toluene fraction of an ethanolic extract of Thapsia garganica fruits). Elution profiles of 10 x 1 mm i.d. SPE cartridges filled with poly(divinylbenzene) resin were found to be only marginally broader than those observed upon direct injection of 6-microL samples into the probe. Thus, the technique focuses analytes emerging in the HPLC elution bands of 0.5-1 mL into volumes of approximately 10 microL, compatible with the CapNMR probe. Using this technique, nine natural products (1-9) present in the plant extract in amounts varying from 0.1 to 20% were identified by means of 1D and 2D NMR spectra, supported by parallel HPLC-ESIMS measurements. Therefore, HPLC-SPE-CapNMR should be regarded as an attractive alternative to other applications of CapNMR for mixture analysis.