A study of comparability in amplified fragment length polymorphism profiling using a simple model system

A simple amplified fragment length polymorphism (AFLP) model, using the bacteriophage lambda genome, was developed to test the reproducibility of this technique in an international comparative study. Using either non-selective or selective primers, nine fragments or subsets of two or three fragments, respectively, were predicted using in silico software. Under optimized conditions, all predicted fragments were experimentally generated. The reproducibility of the AFLP model was tested by submitting both "unknown" DNA template that had been restricted and ligated with AFLP linkers (R/L mixture) and corresponding primer pairs to nine laboratories participating in the study. Participants completed the final PCR step and then used either slab gel electrophoresis or CE to detect the AFLP fragments. The predicted fragments were identified by the majority of participants with size estimates consistently up to 3 base pair (bp) larger for slab gel electrophoresis than for CE. Shadow fragments, 3 bp larger than the predicted fragments, were often observed by study participants and organizers. The nine AFLP fragments exhibited relative intensities ranging from less than 3% to 22% and, apart from the two weakest fragments, with a % CV of 16 to 25. Fragments containing the highest guanine-cytosine (GC) content of 50-56% showed the greatest stability in the AFLP profiles.     

Reference materials to evaluate measurement systems for the nutrient composition of foods: results from USDA’s National Food and Nutrient Analysis Program (NFNAP)

Over a 6.5-year period a total of 2554 values were reported by nine laboratories for 259 certified or reference nutrient concentrations in 26 certified reference materials (CRM) submitted to contract laboratories, blinded, as part of the qualifying process for analytical contracts and in the routine sample stream as part of the National Food and Nutrient Analysis Program. Each value was converted to a Z′-score, reflecting the difference from the assigned value related to the combined expected analytical uncertainty plus the uncertainty in the CRM value. Z′-scores >|3.0| were considered unacceptable. For some nutrients (Na, folate, dietary fiber, pantothenic acid, thiamin, tocopherols, carotenoids, monounsaturated, and polyunsaturated fatty acids), >20% of Z′-scores were >|3.0|. For total fat, vitamin C, and niacin >25% of Z′-scores were >|2.0|. Components for which CRM data were best (more than 90% of Z′-scores <|2.0|) were Mg, P, Mn, Se, and vitamin B12. In some cases deviations from assigned values were not uniform across laboratories and materials. For Na almost all high Z′-scores were for low-Na matrices, suggesting analytical problems related to concentration. Figure Z′-scores for vitamins in certified reference materials Disclaimer: Certain commercial equipment, instruments, or materials are identified in this paper in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by the National Institute of Standards and Technology, or the United States Department of Agriculture, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose.     

The caffeine contents of dietary supplements commonly purchased in the US: analysis of 53 products with caffeine-containing ingredients

As part of a study initiating the development of an analytically validated Dietary Supplement Ingredient Database (DSID) in the United States (US), a selection of dietary supplement products were analyzed for their caffeine content. Products sold as tablets, caplets, or capsules and listing at least one caffeine-containing ingredient (including botanicals such as guarana, yerba mate, kola nut, and green tea extract) on the label were selected for analysis based on market share information. Two or three lots of each product were purchased and analyzed using high-pressure liquid chromatography (HPLC). Each analytical run included one or two National Institute of Standards and Technology (NIST) Standard Reference Materials (SRMs) and two products in duplicate. Caffeine intake per serving and per day was calculated using the maximum recommendations on each product label. Laboratory analysis for 53 products showed product means ranging from 1 to 829 mg caffeine/day. For products with a label amount for comparison (n = 28), 89% (n = 25) of the products had analytically based caffeine levels/day of between −16% and +16% of the claimed levels. Lot-to-lot variability (n = 2 or 3) for caffeine in most products (72%) was less than 10%.     

Measuring vitamins and minerals in dietary supplements for nutrition studies in the USA

This article illustrates the importance of having analytical data on the vitamin and mineral contents of dietary supplements in nutrition studies, and describes efforts to develop an analytically validated dietary supplement ingredient database (DSID) by a consortium of federal agencies in the USA. Preliminary studies of multivitamin mineral supplements marketed in the USA that were analyzed as candidates for the DSID are summarized. Challenges are summarized, possible future directions are outlined, and some related programs at the Office of Dietary Supplements, National Institutes of Health are described. The DSID should be helpful to researchers in assessing relationships between intakes of vitamins and minerals and health outcomes.     

Conservation laws with a random source

We study the scalar conservation law with a noisy nonlinear source, namely,u _l + f(u)_x = h(u, x, t) + g(u)W(t), whereW(t) is the white noise in the time variable, and we analyse the Cauchy problem for this equation where the initial data are assumed to be deterministic. A method is proposed to construct approximate weak solutions, and we then show that this yields a convergent sequence. This sequence converges to a (pathwise) solution of the Cauchy problem. The equation can be considered as a model of deterministic driven phase transitions with a random perturbation in a system of two constituents. Finally we show some numerical results motivated by two-phase flow in porous media. This research has been supported by VISTA (a research cooperation between the Norwegian Academy of Science and Letters and Den norske stats oljeselskap, Statoil) and NAVF (the Norwegian Research Council for Science and the Humanities).     

The application of gas barrier and thermal expansion techniques to study structural changes on annealing

Changes occur in the structure of drawn polyethylene when it is annealed at temperatures close to that of the drawing process. Measurements have been made of the oxygen barrier properties and of the thermal expansion coefficient in the draw direction on samples over a wide draw ratio range both before and after annealing at various temperatures. The results are augmented by density, creep modulus, and shrinkage observations. All samples show a drop in the barrier properties and an increase in the thermal expansion after annealing. However, whereas high-draw-ratio samples show relatively small effects, the changes observed at low draw ratios are very large, with some barrier properties even lower than those of the isotropic feedstock. The effects are larger at the higher annealing temperatures. The diffusion and expansion measurements are greatly influenced by the amorphous regions in the polymer; these results are interpreted as a relaxation of internal stresses giving rise to greater accessibility of the intercrystalline regions. Further experimental work is required to exploit these techniques.     

Probing the solvent accessibility and electron density of adenine: oxidation of 7-deazaadenine in bent DNA and purine doublets

The effect of DNA bending on nucleobase electron transfer was investigated by studying the oxidation of double-stranded sequences containing seven repeats of the known bent sequence d(GGCA(1)A(2)A(3)A(4)A(5)A(6)C) where 7-deazaadenine (zA) was substituted at the A(3) position. Native gel electrophoresis was used to show that the sequence remained bent upon substitution of zA, which provides for oxidation of the sequence by Ru(bpy)(3)(3+) (bpy = 2,2'-bipyridine). The Ru(III) oxidant was generated by photolysis of Ru(bpy)(3)(2+) in the presence of ferricyanide, and the oxidation was visualized by high-resolution gel electrophoresis of the radiolabeled DNA sequence following base treatment. Cleavage of the DNA strand at the guanine residues and at the zA residues was observed. Comparison of the oxidation of zA in bent DNA versus the normal B form showed that hybridization of the B form sequence to its Watson-Crick complement produced a reduction in cleavage by a factor of 5.19 +/- 0.46 while hybridization of the bent sequence only reduced cleavage by a factor of 1.58 +/- 0.23. This result implies that the zA in the double-stranded, bent sequence is much more solvent-exposed than in normal B-form DNA. When the zA occurred in a B-form 5'-zA-G doublet, the reactivity was 6.63 +/- 0.10 times higher for the zA compared to the G. This implies an even greater effect of a 3'-guanine on the oxidation potential of zA than in the well-known 5'-GG doublet.     

Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry

A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and mu LC-MS/MS is presented. 100% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by mu LC-MS/MS while 97% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip(C18) and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (<23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using mu LC-MS/MS, 50% of the spots analyzed were identified as containing multiple proteins. mu LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by mu LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50% for approximately 70% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins.