Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes

Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays.     

Determination of dithiocarbamate fungicide residues in food by a spectrophotometric method using a vertical disulfide reaction system

Dithiocarbamates are a class of fungicides extensively used in many crops worldwide. The current residue definition of dithiocarbamates in food for compliance with maximum residue limits, at national and international levels, is total residues arising from the use of any or each dithiocarbamate fungicide, determined as CS(2). The analytical method most frequently used to analyze dithiocarbamate residues in food for monitoring purposes was proposed more than 30 years ago. In this method, total dithiocarbamates are decomposed to CS(2), which is purified and reacted with a cupric reagent. The yellow complex formed is quantified by spectrophotometry. In this paper, a new reaction system for the purification and complexation of CS(2) is proposed. The new system is less fragile than the traditional design, is easier to assemble, and allows for a higher sample throughput, in addition to being of low cost. Recovery of added mancozeb, thiram, or ziram (0.15-8.0 mg/kg) in rice, beans, apple, banana, orange, papaya, tomato, cucumber, and potato ranged from 82 to 120%, with relative standard deviations from 0 to 10% (n = 3 or 5). Analysis of apple, tomato, and papaya samples with field-incurred dithiocarbamate residues showed comparable results using both the traditional and the new reaction systems.     

Detection of genetically modified soybean using peptide nucleic acids (PNAs) and microarray technology

Peptide nucleic acid (PNA) microarrays for the detection of Roundup Ready soybeans in food have been prepared. PNA probes are known to be more efficient and selective in binding DNA sequences than the analogous oligonucleotides and are very suitable to be used for diagnostics in food. PNAs of different lengths were carefully designed and synthesized by solid-phase synthesis on an automatic synthesizer adopting the BOC strategy. PNAs were purified by HPLC and characterized by HPLC/MS. The probes were spotted on a functionalized surface to produce a microarray to be hybridized with PCR products. DNA extracted from reference material was amplified using Cy3- and Cy5-labeled primers, and the fluorescent PCR products obtained were hybridized on the microarray. Two protocols were adopted: the hybridization with dsDNA or with ssDNA obtained by digestion with the enzyme lambda exonuclease. The best results were obtained using a 15-mer PNA probe in combination with the ssPCR product derived from enzymatic digestion. The method was applied to the analysis of a sample of certified transgenic soybean flour.     

Precolumn phenylisothiocyanate derivatization and liquid chromatography of amino acids in food

A precolumn phenylisothiocyanate derivatization method is described for the determination of amino acids in protein hydrolysates from a wide variety of complex food matrixes, with and without performic acid oxidation pretreatment. Analysis of samples that were not pretreated with performic acid was necessary since this pretreatment destroyed an average of 25% of the histidine and 87% of the tyrosine present in the food samples. This method is rapid and reproducible; coefficients of variation between duplicate analyses of the same food item were less than 5% for a majority of the amino acids. Occasionally, variation between duplicate analyses for histidine and tyrosine was greater than 10%. Recoveries of amino acids added to samples were in the 100% range.     

Detection and identification of beta-lactam residues in milk using a hybrid biosensor

A novel application of a hybrid biosensor is here employed as an analytical method for the detection and presumptive identification of beta-lactam residues in milk. The method is based on measurements of carbon dioxide (CO2), the production of which is related to the microbial growth of the test microorganism Bacillus stearothermophilus var. calidolactis. The presence of beta-lactams in milk inhibits microbial growth and, consequently, the CO2 production rate. The analysis is based on the variation of CO2 between a milk sample spiked with beta-lactams and a twin milk sample containing beta-lactams plus a broad spectrum beta-lactamase, using an electrochemical device of biosensor. A blank milk sample is included as control. The result is obtained starting from the first 120 min. Moreover, the ability to recognize all of the beta-lactams speeds the total time of analysis when chemical identification and quantification are required. The analytical method appears to be adequate for milk control for qualitative screening purposes, complying with the requirements stated in Decision 2002/657/EC.     

HPLC method for analysis of free amino acids in fish using o-phthaldialdehyde precolumn derivatization

Precolumn derivatization applying o-phthaldialdehyde (OPA) was used to analyze free lysine, histidine, and ornithine, precursors of the respective biogenic amines cadaverine, histamine, and putrescine, which are considered indicators of fish quality and safety. This method uses 75% methanol to eliminate the use of strong acids as the extraction solution. Each analysis took 35 min, was reproducible, and allowed separation of primary amino acids in fish samples. A binary solvent delivery system coupled with a fluorescence detector and an Ultrasphere ODS column were utilized for HPLC separation. Linearity of the calibration curves was very good (r(2) = 0.99) for the amino acids of interest. Minimum concentrations of detection were 40 pmol/mL for histidine and lysine and 70 pmol/mL for ornithine. Average recoveries were 72% for lysine, 93% for histidine, and 98% for ornithine. This method used solvent gradient elution to study the levels of these analytes in mahi-mahi, bigeye tuna, and flounder.     

Detection of potentially allergenic hazelnut (Corylus avellana) residues in food: a comparative study with DNA PCR-ELISA and protein sandwich-ELISA

Allergen detection is of increasing interest for food labeling purposes. A comparative study with a commercial hazelnut-specific PCR-ELISA and a sandwich-type ELISA detecting hazelnut protein was performed to investigate to what extent immunochemical and DNA-based techniques would correlate in the detection of trace amounts of potentially allergenic hazelnut residues. Both methods were highly sensitive and allowed the detection of even <10 ppm of hazelnut in complex food matrixes. The protein-ELISA was highly specific for hazelnut. However, some foods could lead to false-positive results at the 10 ppm level. The PCR-ELISA did not show any cross-reactions with non-hazelnut foods, thus reducing the probability of having false positives at the trace level. Forty-one commercial food products with and without hazelnut components on their labels were analyzed for the presence of hazelnut. Of the 27 products in which hazelnut components were detected, two samples were not identified by the protein-ELISA, and only one sample, namely one white chocolate having <1 ppm of hazelnut protein, was not detected by PCR-ELISA. The good correlation of the results of PCR-ELISA and protein-ELISA suggested that both PCR-based and immunochemical techniques are suitable for reliable detection of potentially allergenic hazelnut residues in foods at the trace level.     

Polyphenolic compounds interfere with quantification of protein in soil extracts using the Bradford method

 The Bradford protein quantification assay is based on an absorbance shift in Coomassie brilliant blue G-250 (CBB). Samples extracted for glomalin, a protein produced by arbuscular mycorrhizal (AM) fungi, are quantified using the Bradford assay. CBB is known to react with polyphenolic substances, and co-extraction of glomalin and humic substances is known to occur. The effects of increasing concentrations polyphenolic compounds were measured. The addition of any amount of polyphenolic compounds increased the Bradford reactive fraction (BRF) of soil extract. Caution is required when interpreting BRF data, as comparison of BRF data from different studies or different field sites is problematic. The BRF may represent recalcitrant organic material in soil, though its relationship to AM fungi remains unclear.     

The role of amino acids and nucleic bases in turnover of nitrogen and carbon in soil humic fractions

Incorporation of labelled ¹⁵N and ¹⁴C amino acids and nucleic bases into soil humus fractions as well as humus turnover was investigated under field conditions. The dynamics of ¹⁵N and ¹⁴C incorporation into organic matter was characterized by the following main steps: rapid incorporation of the labelled substance prevailing for the first 1–3 weeks, and decomposition of included labelled fragments prevailing beyond one month after substance addition. The annual turnover rates of N and C in humus fractions due to incorporation of amino acids and nucleic bases were calculated. The turnover rate of N in humus is two to three times that of C. The contribution of amino acids to organic matter generation is about twice as great as that of nucleic bases and other N-containing organic substances. This indicates the important role of amino acids in the humification process and humus turnover. Turnovers of humic acids (0·002 year^?1 for C and 0·02 for N) are the most rapid of humic fractions investigated, and humin is characterized by the slowest turnover (0·0002 year^?1 for C and 0·007 for N). There are no significant differences in the turnover rates of fulvic acid fractions (0·0002 year^?1 for C) with different molecular weight.     

Rapid and sensitive quantification of amino acids in soil extracts by capillary electrophoresis with laser-induced fluorescence

A growing body of research is arguing that amino acids are key components of the soil nitrogen cycle. For example, we now know that many plants can take up intact amino acids, even in competition with soil microbes. Our growing recognition of the importance of amino acids is not matched by knowledge of the amounts and type of amino acids in the soil, certainly not in comparison with our encyclopaedic knowledge of inorganic N. The primary reason that less is known about amino acids than inorganic N is that measuring the amounts of individual amino acids with conventional chromatographic techniques is slow and typically requires extensive sample clean-up if KCl extracts are analysed. The aim of this study was to develop capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) as a more rapid alternative for measuring individual amino acids in KCl extracts of soil. The CE-LIF method separated 17 common amino acids within 12 min, with detection limits between 7 and 250 nM. One molar KCl extracts could be analysed without any sample clean-up or de-salting, and spike and recovery tests indicated that the complex matrix of soil extracts did not affect quantification. Further evidence of the suitability and robustness of the method came from the repeated analysis (n=5) of the same soil KCl extract. The relative standard deviation of migration times for replicate analyses were <0.2% while relative standard deviations for peak areas were <5%. To demonstrate application of the CE-LIF method to real world problems it was used to analyse amino acids in 1 M KCl extracts from a sub-alpine grassland and a Eucalyptus regnans forest. The most abundant amino acids were Ala, Gly and Arg. Other amino acids present at smaller concentrations or in a minority of samples were Asn, Cit, GABA, Glu, His, Phe, Leu, and Lys. The proposed CE-LIF method offers significant advantages over chromatographic methods via its rapidity, reproducibility and, most importantly, its ability to analyse crude KCl extracts.     

A novel in situ water perfusion and extraction method for soil amino acid quantification

Classic methods of soil amino acid (SAA) determination involve field collection of soils and disturbance during storage, sieving, mixing and extraction in the laboratory. We describe a novel inexpensive method for extraction of SAA's in situ with minimal soil disturbance. In a comparison between methods of SAA extraction from a semiarid grassland site, glu-x and arginine were the dominant SAA nitrogen sources detected by the novel method while serine and glycine were the dominant SAA nitrogen sources detected using the classic method. The extraction method employed is likely to be useful for accurate determination of SAA availability to plants and soil microbes.     

A new, rapid, high-sensitivity analysis of amino acids in food type samples

A new approach to the analysis of free amino acids and amino acids from hydrolyzed foods is described. The method is based on reaction of the free amino acids with phenylisothiocyanate to form stable derivatives which are subsequently separated by liquid chromatography. Sample preparation procedures are described and results are compared with conventional ion exchange results. Reproducibility of the new method has been determined on a typical food type sample.     

Oxidation and hydrolysis determination of sulfur amino acids in food and feed ingredients: collaborative study

Samples of 6 food and feed ingredients and a purified protein, beta-lactoglobulin, were analyzed by 7 laboratories to determine the concentrations of cysteine as cysteic acid and methionine as methionine sulfone. Samples were oxidized by reaction with performic acid before hydrolysis with 6N HCl. The free amino acids were then separated and measured by ion-exchange chromatography on dedicated amino acid analyzers. Each laboratory was provided with a detailed method as well as sealed vials containing solutions of standards. For the determination of cysteine as cysteic acid, the coefficients of variation between laboratories for duplicate samples ranged from 7.13 to 10.8% for the 6 ingredients. For the determination of methionine as methionine sulfone, the coefficients of variation between laboratories for duplicate samples ranged from 1.18 to 12.8% for the 6 ingredients. Cysteine and methionine recoveries were determined by analysis of beta-lactoglobulin and were based on expected levels of each amino acid from amino acid sequence data. The mean recovery of cysteine was 95% with a range of 91-101%. The mean recovery of methionine was 101% with a range of 98-106%. This method has been adopted official first action.     

Determination of sulfur amino acids and tryptophan in foods and food and feed ingredients: collaborative study

Samples of 4 foods, 1 animal feed, isolated soy protein, and beta-lactoglobulin were analyzed by 9 laboratories to determine concentrations of cysteine as cysteic acid, methionine as methionine sulfone, and tryptophan. Sulfur amino acids were determined by AOAC method 43.A08-43.A13 for food and feed ingredients, in which samples are oxidized with performic acid before protein hydrolysis with 6N HCl. Tryptophan was determined after protein hydrolysis with 4.2N NaOH. In both methods, free amino acids were separated by ion-exchange or reverse-phase chromatography. Each laboratory was provided with detailed methods and with sealed vials containing solutions of standards. Samples were analyzed in duplicate, and variation between laboratories was determined. Coefficients of variation between laboratories for the 6 samples ranged from 5.50 to 11.8% for methionine as methionine sulfoxide, 8.59 to 17.3% for cysteine as cysteic acid, and 3.87 to 16.1% for tryptophan. Amino acid recoveries were determined by analysis of beta-lactoglobulin and were based on expected levels of each amino acid obtained from amino acid sequence data. The mean recovery of cysteine was 97% with a range of 88-119%. For methionine, mean recovery was 98% (range 89-115%) and for tryptophan, 85% (range 59-102%). Method 43.A08-43.A13 for food and feed ingredients has been adopted official first action for determination of cysteine and methionine in processed foods. The alkaline hydrolysis method has been adopted official first action for determination of tryptophan in foods and food and feed ingredients.     

Retention of essential amino acids during extrusion of protein and reducing sugars

This research investigates the retention of essential amino acid profiles of products during the extrusion of proteins and reducing sugars. Animal proteins (egg and milk protein at 10 and 30% levels) and reducing sugars (fructose and galactose at 0, 2, and 8% levels), with pregelatinized wheat flour, were extruded at 110 and 125 degrees C product temperatures and feed moistures of 19 and 23.5% for egg protein and 13.75 and 16% for milk protein. The nutritional property analyzed was essential amino acid retention, and sugar retention was also considered to understand the relationship of sugars with retention of amino acids. Lysine showed the lowest retention (up to 40%) of all the essential amino acids. Retention of other essential amino acids varied from 80 to 100% in most situations. Apart from lysine, tryptophan, threonine, and methionine were found to be significantly changed ( P < 0.05) with processing conditions. Increased protein and sugar levels resulted in a significant degradation of lysine. Greater lysine retention was found at a lower temperature and higher feed moisture. Results of sugar retention also showed similar patterns. The products made from fructose had greater lysine retention than products made from galactose with any type of protein. The outcomes of this research suggested that the combination of milk protein and fructose at a lower temperature and higher feed moisture is most favorable for developing high-protein extruded products.     

Gas chromatography-mass spectrometry method for the determination of free amino acids as their dimethyl-tert-butylsilyl (TBDMS) derivatives in animal source food

The suitability of a one-step derivatization procedure using N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide for the simultaneous assay of 22 free amino acids and its application for their analysis in six animal source foods (pork, dry cured ham, chicken stock, fresh cheese, ripened cheese, and dry salted sardine) by GC-MS were studied. All 22 free amino acid derivatives were correctly detected and resolved. Reproducibility (%RSD) of the method was in the range of 1.9-12.2%. Detection and quantitation limits of the analytical procedure ranged from 0.01 to 0.46 mg/100 g dry weight and from 0.02 to 1.55 mg/100 g dry weight, respectively. The calibration curves were linear within the range 0.1-15.0 mg/100 g with correlation coefficient values (R(2)) from 0.9891 to 0.9983. All analyzed food products showed free amino acid contents similar to those found in the scientific literature. The proposed GC-MS method for the determination of free amino acids in animal source food can be used in routine for both analytical and research purposes.     

Development of a new methanethiol quantification method using ethanethiol as an internal standard

Development of a new method to quantify methanethiol in which ethanethiol was employed as an internal standard is reported. Recovery yields for methanethiol from an aqueous model system and a soy protein concentrate (SPC) aqueous slurry determined with this method ranged from 97 to 107% and from 103 to 121%, respectively. The methanethiol content of two commercial SPCs and two commercial soy protein isolate (SPI) samples, on a dry basis, ranged from 835 to 1190 times greater than the odor threshold for methanethiol. Relative standard deviations for quantifying methanethiol with the method from these samples were <5%, indicating its good reproducibility in quantifying methanethiol from soy protein products. Also investigated in the current study was the feasibility of using 5',5-dithiobis(2-nitrobenzoic acid) (DTNB, Ellman's reagent) to determine the concentration of methanethiol in the aqueous solutions used to prepare the standard curve for quantifying methanethiol from soy protein products. The concentrations of methanethiol obtained from Ellman's reagent method were comparable with those from a weighing method and theoretical calculation.