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  • Polymorphism/mutation detection  (4)
  • Beverages  (3)
  • Oxford University Press  (7)
  • Wiley
  • 2015-2019
  • 2010-2014  (7)
  • 1980-1984
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  • 2012  (7)
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  • 1
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    Maximizing signal-to-noise ratio in the random mutation capture assay (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-14
    Description: The ‘Random Mutation Capture’ assay allows for the sensitive quantitation of DNA mutations at extremely low mutation frequencies. This method is based on PCR detection of mutations that render the mutated target sequence resistant to restriction enzyme digestion. The original protocol prescribes an end-point dilution to about 0.1 mutant DNA molecules per PCR well, such that the mutation burden can be simply calculated by counting the number of amplified PCR wells. However, the statistical aspects associated with the single molecular nature of this protocol and several other molecular approaches relying on binary (on/off) output can significantly affect the quantification accuracy, and this issue has so far been ignored. The present work proposes a design of experiment (DoE) using statistical modeling and Monte Carlo simulations to obtain a statistically optimal sampling protocol, one that minimizes the coefficient of variance in the measurement estimates. Here, the DoE prescribed a dilution factor at about 1.6 mutant molecules per well. Theoretical results and experimental validation revealed an up to 10-fold improvement in the information obtained per PCR well, i.e. the optimal protocol achieves the same coefficient of variation using one-tenth the number of wells used in the original assay. Additionally, this optimization equally applies to any method that relies on binary detection of a small number of templates.
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Direct, genome-wide assessment of DNA mutations in single cells (2012)
    Oxford University Press
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    Publication Date: 2012-03-14
    Description: DNA mutations are the inevitable consequences of errors that arise during replication and repair of DNA damage. Because of their random and infrequent occurrence, quantification and characterization of DNA mutations in the genome of somatic cells has been difficult. Random, low-abundance mutations are currently inaccessible by standard high-throughput sequencing approaches because they cannot be distinguished from sequencing errors. One way to circumvent this problem and simultaneously account for the mutational heterogeneity within tissues is whole genome sequencing of a representative number of single cells. Here, we show elevated mutation levels in single cells from Drosophila melanogaster S2 and mouse embryonic fibroblast populations after treatment with the powerful mutagen N -ethyl- N -nitrosourea. This method can be applied as a direct measure of exposure to mutagenic agents and for assessing genotypic heterogeneity within tissues or cell populations.
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Stop or go? How is the UK food industry responding to front-of-pack nutrition labels? (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-30
    Description: The adoption of voluntary front-of-pack (FOP) nutrition labels by UK food retailers and manufacturers is explored. These labels highlight key nutrients, facilitating product comparisons. Information for 2,201 products launched between 2007 and 2009 was analysed. Binary and multinomial logistic regression models explore drivers of FOP label use. Products introduced more recently by retailers and certain food categories were more likely to carry FOP labels. Increasing the content of sodium and sugar decreased odds of FOP use in some categories, but with limited significance. Discussion includes policy options to optimise firm response and implications for evolving mandatory FOP labelling proposals.
    Keywords: L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 4
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    Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-08
    Description: The utilization of archived, formalin-fixed paraffin-embedded (FFPE) tumor samples for massive parallel sequencing has been challenging due to DNA damage and contamination with normal stroma. Here, we perform whole genome sequencing of DNA isolated from two triple-negative breast cancer tumors archived for 〉11 years as 5 µm FFPE sections and matched germline DNA. The tumor samples show differing amounts of FFPE damaged DNA sequencing reads revealed as relatively high alignment mismatch rates enriched for C·G 〉 T·A substitutions compared to germline samples. This increase in mismatch rate is observable with as few as one million reads, allowing for an upfront evaluation of the sample integrity before whole genome sequencing. By applying innovative quality filters incorporating global nucleotide mismatch rates and local mismatch rates, we present a method to identify high-confidence somatic mutations even in the presence of FFPE induced DNA damage. This results in a breast cancer mutational profile consistent with previous studies and revealing potentially important functional mutations. Our study demonstrates the feasibility of performing genome-wide deep sequencing analysis of FFPE archived tumors of limited sample size such as residual cancer after treatment or metastatic biopsies.
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Functional foods as differentiated products: the Italian yogurt market (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Description: In spite of the growing consumers' interest for functional foods, the knowledge regarding the demand for these products and their profitability is limited. Adapting the LA/AIDS (Linear Approximated–Almost Ideal Demand System) model by means of Pinkse, Slade and Brett's distance metric method (2002), this article studies demand, substitution pattern, and profitability of conventional and functional alternatives inside the yogurt category in Italy. Results indicate that, in the yogurt market, functional alternatives' demand is often less elastic than that of their conventional counterparts, that brand loyalty plays a key role, and that the profitability of the functional alternatives is, on average, larger than that of conventional ones.
    Keywords: L11 - Production, Pricing, and Market Structure ; Size Distribution of Firms, L13 - Oligopoly and Other Imperfect Markets, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 6
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    Network externalities in supermarket retailing (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Description: Supermarkets face a two-sided demand for shelf space: consumers demand variety and suppliers demand shelf space. We exploit the asymmetric ability of consumers and suppliers to internalise network effects to derive a novel test of network effects in multi-product retail markets. Because consumers fully internalise network effects but suppliers cannot, retail margins rise and wholesale margins fall as variety increases. We test this hypothesis using retail scanner data for a ‘shopping basket’ of items from competing retailers using a structural model of retail variety and vertical pricing. Our results support the existence of positive, two-sided network effects in supermarket retailing.
    Keywords: C35 - Discrete Regression and Qualitative Choice Models, L11 - Production, Pricing, and Market Structure ; Size Distribution of Firms, L13 - Oligopoly and Other Imperfect Markets, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, L81 - Retail and Wholesale Trade ; e-Commerce
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 7
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    Fluorescent signatures for variable DNA sequences (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-25
    Description: Life abounds with genetic variations writ in sequences that are often only a few hundred nucleotides long. Rapid detection of these variations for identification of genetic diseases, pathogens and organisms has become the mainstay of molecular science and medicine. This report describes a new, highly informative closed-tube polymerase chain reaction (PCR) strategy for analysis of both known and unknown sequence variations. It combines efficient quantitative amplification of single-stranded DNA targets through LATE-PCR with sets of Lights-On/Lights-Off probes that hybridize to their target sequences over a broad temperature range. Contiguous pairs of Lights-On/Lights-Off probes of the same fluorescent color are used to scan hundreds of nucleotides for the presence of mutations. Sets of probes in different colors can be combined in the same tube to analyze even longer single-stranded targets. Each set of hybridized Lights-On/Lights-Off probes generates a composite fluorescent contour, which is mathematically converted to a sequence-specific fluorescent signature. The versatility and broad utility of this new technology is illustrated in this report by characterization of variant sequences in three different DNA targets: the rpoB gene of Mycobacterium tuberculosis, a sequence in the mitochondrial cytochrome C oxidase subunit 1 gene of nematodes and the V3 hypervariable region of the bacterial 16 s ribosomal RNA gene. We anticipate widespread use of these technologies for diagnostics, species identification and basic research.
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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