A radial calibration window for analytical ultracentrifugation

Analytical ultracentrifugation (AUC) is a first-principles based method for studying macromolecules and particles in solution by monitoring the evolution of their radial concentration distribution as a function of time in the presence of a high centrifugal field. In sedimentation velocity experiments, hydrodynamic properties relating to size, shape, density, and solvation of particles can be measured, at a high hydrodynamic resolution, on polydisperse samples. In a recent multilaboratory benchmark study including data from commercial analytical ultracentrifuges in 67 laboratories, the calibration accuracy of the radial dimension was found to be one of the dominant factors limiting the accuracy of AUC. In the present work, we develop an artifact consisting of an accurately calibrated reflective pattern lithographically deposited onto an AUC window. It serves as a reticle when scanned in AUC control experiments for absolute calibration of radial magnification. After analysis of the pitch between landmarks in scans using different optical systems, we estimate that the residual uncertainty in radial magnification after external calibration with the radial scale artifact is ≈0.2 %, of similar magnitude to other important contributions after external calibration such as the uncertainty in temperature and time. The previous multilaboratory study had found many instruments with errors in radial measurements of 1 % to 2 %, and a few instruments with errors in excess of 15 %, meaning that the use of the artifact developed here could reduce errors by 5-to 10-fold or more. Adoption of external radial calibration is thus an important factor for assuring accuracy in studies related to molecular hydrodynamics and particle size measurements by AUC.

Effects of acidification, lipid removal and mathematical normalization on carbon and nitrogen stable isotope compositions in beaked whale (Ziphiidae) bone

RATIONALE

The analysis of stable isotopes in tissues such as teeth and bones has been used to study long-term trophic ecology and habitat use in marine mammals. However, carbon isotope ratios (δ(13) C values) can be altered by the presence of (12) C-rich lipids and carbonates. Lipid extraction and acidification are common treatments used to remove these compounds. The impact of lipids and carbonates on carbon and nitrogen isotope ratios (δ(15) N values), however, varies among tissues and/or species, requiring taxon-specific protocols to be developed.

METHODS

The effects of lipid extraction and acidification and their interaction on carbon and nitrogen isotope values were studied for beaked whale (Ziphiidae) bone samples. δ(13) C and δ(15) N values were determined in quadruplicate samples: control, lipid-extracted, acidified and lipid-extracted followed by acidification. Samples were analyzed by means of elemental analysis isotope ratio mass spectrometry. Furthermore, the efficiency of five mathematical models developed for estimating lipid-normalized δ(13) C values from untreated δ(13) C values was tested.

RESULTS

Significant increases in δ(13) C values were observed after lipid extraction. No significant changes in δ(13) C values were found in acidified samples. An interaction between both treatments was demonstrated for δ(13) C but not for δ(15) N values. No change was observed in δ(15) N values for lipid-extracted and/or acidified samples. Although all tested models presented good predictive power to estimate lipid-free δ(13) C values, linear models performed best.

CONCLUSIONS

Given the observed changes in δ(13) C values after lipid extraction, we recommend a priori lipid extraction or a posteriori lipid normalization, through simple linear models, for beaked whale bones. Furthermore, acidification seems to be an unnecessary step before stable isotope analysis, at least for bone samples of ziphiids. Copyright © 2015 John Wiley & Sons, Ltd.

[Biases on community structure during DNA extraction of shrimp intestinal microbiota revealed by high-throughput sequencing]

OBJECTIVES

High-throughput sequencing technology is increasingly applied in intestinal microbiota of aquatic animals including shrimp. However, there is a lack of standard method or kit for DNA isolation from shrimp intestinal microbiota, and little is known about the effectiveness and biases regarding DNA extraction based on high-throughput sequencing. The aim of this study was to study the biases of different DNA extraction kits on community structure of shrimp intestinal microbiota through high-throughput sequencing, and to better understand the structure and composition of bacterial flora associated with healthy Litopenaeus vannamei.

METHODS

We extracted the total DNA of intestinal microbiota from L. vannamei with three commercial kits designed for DNA extraction from bacteria, stool and tissue (Omega, USA). DNA quality was evaluated based on the absorbance ratios of 260/280 nm by NanoDrop, while DNA concentration was quantified using PicoGreen. Then Illumina MiSeq high-throughput sequencing was used to examine the intestinal bacterial communities following PCR amplification of 16S rDNA V4 region.

RESULTS

The yield and purity of the DNA from the Bacterial Kit (SIB) were superior to those from the Stool Kit (SIS), whereas the DNA from Tissue Kit (SIT) presented too small amount to be amplified efficiently. The average sequence reads obtained from SIB and SIS samples were 52151 ± 5085 and 55296 ± 5147 respectively. After resampling at the same depth of 46800 reads, the operational taxonomic unit (OTU) number and Shannon diversity index of SIS samples were significantly higher than those of SIB samples. By contrast, the reproducibility of OTU among SIB replicates was higher than that among SIS replicates. The dominant phyla of SIS and SIB samples were identical, including Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, and Cyanobacteria. However, the relative abundances of almost all the dominant groups at various taxonomic levels differed greatly between these two samples.

CONCLUSION

Significant biases on community structure of shrimp intestinal microbiota were detected which originated from DNA extraction. And the core microbiota of the healthy L. vannamei in this study was mainly composed of genera Photobacterium, Lactococcus, Aliivibrio, Vibrio, as well as three other unclassified groups.

Estimation of sampling uncertainty of pesticide residues based on supervised residue trial data

Typical sampling uncertainties were calculated as the average of relative standard deviations (CV) of residues measured in individual crops tested in supervised residue trials and from their pooled variance for crop groups. The relative confidence intervals of the sampling uncertainty for different crops were estimated from the random duplicate composite samples generated with computer modeling from residues in 182 independent primary sample sets, each consisting of 100-320 residue data. The relative 95% confidence intervals were found to be independent from the CV of primary residue data populations; therefore, the calculated values are generally applicable. In view of the potentially serious consequences of underestimated sampling uncertainties, their upper confidence limits are recommended for practical use to verify the compliance of products and for planning statistically based sampling programs. Sampling uncertainties are reported for 24 crop groups and 106 individual crops.

Sampling and sample processing in pesticide residue analysis

Proper sampling and sample processing in pesticide residue analysis of food and soil have always been essential to obtain accurate results, but the subject is becoming a greater concern as approximately 100 mg test portions are being analyzed with automated high-throughput analytical methods by agrochemical industry and contract laboratories. As global food trade and the importance of monitoring increase, the food industry and regulatory laboratories are also considering miniaturized high-throughput methods. In conjunction with a summary of the symposium "Residues in Food and Feed - Going from Macro to Micro: The Future of Sample Processing in Residue Analytical Methods" held at the 13th IUPAC International Congress of Pesticide Chemistry, this is an opportune time to review sampling theory and sample processing for pesticide residue analysis. If collected samples and test portions do not adequately represent the actual lot from which they came and provide meaningful results, then all costs, time, and efforts involved in implementing programs using sophisticated analytical instruments and techniques are wasted and can actually yield misleading results. This paper is designed to briefly review the often-neglected but crucial topic of sample collection and processing and put the issue into perspective for the future of pesticide residue analysis. It also emphasizes that analysts should demonstrate the validity of their sample processing approaches for the analytes/matrices of interest and encourages further studies on sampling and sample mass reduction to produce a test portion.

Interlaboratory assessment of cryomilling sample preparation for residue analysis

The effectiveness of the comminution approach used for bulk field samples limits the size of the subsample that must be extracted and analyzed to ensure an adequately representative and reproducible measurement. In many cases this subsample size restricts the residue method to the use of larger vessel formats, limiting downstream throughput. The introduction of a secondary fine-milling step to this process using a subsample size already known to be representative can further improve sample homogeneity and allow direct method scaling to small high-throughput formats. Dramatic increases in method throughput can then be achieved through the simultaneous processing of numerous samples in parallel. This approach was evaluated across a diverse grouping of crop matrices using two substantially different pesticide types. Both fortified and field-collected samples demonstrated a high degree of precision and reproducibility across laboratories. Additional benefits of this approach include significant reductions in cost and solvent waste generation, as well as improvements in assay quality and transferability.

The use of a xylosylated plant glycoprotein as an internal standard accounting for N-linked glycan cleavage and sample preparation variability

RATIONALE

Traditionally, free oligosaccharide internal standards are used to account for variability in glycan relative quantification experiments by mass spectrometry. However, a more suitable internal standard would be a glycoprotein, which could also control for enzymatic cleavage efficiency, allowing for more accurate quantitative experiments.

METHODS

Hydrophobic, hydrazide N-linked glycan reagents (both native and stable-isotope labeled) are used to derivatize and differentially label N-linked glycan samples for relative quantification, and the samples are analyzed by a reversed-phase liquid chromatography chip system coupled online to a Q-Exactive mass spectrometer. The inclusion of two internal standards, maltoheptaose (previously used) and horseradish peroxidase (HRP) (novel), is studied to demonstrate the effectiveness of using a glycoprotein as an internal standard in glycan relative quantification experiments.

RESULTS

HRP is a glycoprotein containing a xylosylated N-linked glycan, which is unique from mammalian N-linked glycans. Thus, the internal standard xylosylated glycan could be detected without interference to the sample. Additionally, it was shown that differences in cleavage efficiency can be detected by monitoring the HRP glycan. In a sample where cleavage efficiency variation is minimal, the HRP glycan performs as well as maltoheptaose.

CONCLUSIONS

Because the HRP glycan performs as well as maltoheptaose but is also capable of correcting and accounting for cleavage variability, it is a more versatile internal standard and will be used in all subsequent biological studies. Because of the possible lot-to-lot variation of an enzyme, differences in biological matrix, and variable enzyme activity over time, it is a necessity to account for glycan cleavage variability in glycan relative quantification experiments.

Optimization of a novel setup for an on-line study of elemental mercury adsorption by cold-vapor atomic absorption spectrometry

BACKGROUND

The objective of this work was developing a simple and stable time-based on-line setup for assessing the potential of mercury (Hg) vapor adsorption of the commercial sorbents used in air sampling and control operation followed by cold vapor atomic absorption spectrometry (CVAAS).

METHODS

A special designed separation chamber was used where reduction of the injected Hg (II) solution took place. Purge gas passes through this chamber resulting to a prompt release of mercury vapor, purging into the adsorbent that regulated at the desired adsorption temperature. After sorbent saturation, in order to study the adsorption parameters of sorbents (activated carbon and bone char) such as breakthrough time (BTT), and adsorptive capacity, mercury gas stream was passed through the sorbents, directly transport to the CVAAS.

RESULTS

Preliminary experiments concerning the reductant solution showed that SnCl2 offers higher stability than NaBH4. Around the loading range 0.125-2.5 ml min⁻¹ of 100 µg l⁻¹ Hg(II) solution, a linear calibration curve with the equation peak area=0.134; loading flow=-0.017 and a correlation coefficient r=0.996 was obtained, and the detection limit was improved up to c(L)=1 µg l⁻¹. The relative standard deviation of five measurements of lowest flow loading of Hg (II) was RSD=2.8%. The significant differences were observed in the breakthrough time and mercury adsorptive capacity between activated carbon and bone char (P=0.010).

CONCLUSION

This novel setup is suitable for an on-line study of elemental mercury adsorption, determination of breakthrough time and adsorption capacity, and because of its stable performance during all experiments; it can be applied to the time based studies.

Sensitive determination of herbicides in food samples by nonaqueous CE using pressurized liquid extraction

We have developed a method involving extraction with mixtures of solvents under pressure (pressurized liquid extraction (PLE)) for the determination of triazine herbicides in a series of samples from the food industry. The organic extracts obtained were subjected to a clean-up step with SPE, using Oasis MCX sorbents, after which they were analyzed by NACE. Potato was chosen as a representative matrix of horticultural products since it has a high water content. Spiked potato samples were used to optimize extraction conditions. In order to compare the results obtained with NACE, different studies were also conducted using HPLC. The detection limits in NACE were similar to those found with HPLC and were of the order of 10-15 microg/kg, depending on the analyte. Satisfactory results were obtained on applying the method proposed for the potato matrix (PLE with separation by electrophoresis) to other food matrices such as other tubercles, fruits, vegetables and cereals.

Fiducial-less alignment of cryo-sections

Cryo-electron tomography of vitreous sections is currently the most promising technique for visualizing arbitrary regions of eukaryotic cells or tissue at molecular resolution. Despite significant progress in the sample preparation techniques over the past few years, the three dimensional reconstruction using electron tomography is not as simple as in plunge frozen samples for various reasons, but mainly due to the effects of irradiation on the sections and the resulting poor alignment. Here, we present a new algorithm, which can provide a useful three-dimensional marker model after investigation of hundreds to thousands of observations calculated using local cross-correlation throughout the tilt series. The observations are chosen according to their coherence to a particular model and assigned to virtual markers. Through this type of measurement a merit figure can be calculated, precisely estimating the quality of the reconstruction. The merit figures of this alignment method are comparable to those obtained with plunge frozen samples using fiducial gold markers. An additional advantage of the algorithm is the implicit detection of areas in the sections that behave as rigid bodies and can thus be properly reconstructed.

Quantification of estrogenic mycotoxins at the ng/L level in aqueous environmental samples using deuterated internal standards

Because of their pronounced estrogenicity, resorcyclic acid lactones (RALs) are of concern in aqueous environments even at the low ng/L level. Therefore, we developed an accurate, precise and sensitive HPLC-MS/MS method to detect these mycotoxins in different aqueous environmental samples. The compounds investigated included zearalenone (ZON), alpha- and beta-zearalenol, zearalanone as well as alpha- and beta-zearalanol. The use of isotope labelled internal standards (in this case deuterated RAL-analogues) ensured an accurate quantification of the target analytes, independent of matrix compounds interfering with the analytes during ionisation and analyte losses occurring during sample preparation. Sample enrichment was carried out by solid-phase extraction (SPE) using Supelclean Envi-18 cartridges. Absolute method recoveries for all analytes ranged from 95 to 108%, 70 to 102%, and 76 to 109%, method detection limits from 0.5 to 2.1 ng/L, 0.4 to 1.1 ng/L, and 0.8 to 12.4 ng/L and precision from 3 to 14%, 2 to 13% and 4 to 16% in drainage water, river water and wastewater treatment plant (WWTP) effluent, respectively. The method was applied to verify the emission of RALs from a Fusarium graminearum infested crop field into the drainage system. Zearalenone was present in drainage water in concentrations up to 30 ng/L. So far, none of the other five investigated compounds have been detected.