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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 100 (2000), S. 256-262 
    ISSN: 1432-2242
    Keywords: Key words Lycopersicon hirsutum ; Lycopersicon esculentum ; PCR ; Fructose ; Glucose
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A genetic trait determining the ratio of fructose to glucose in mature tomato fruits is described. A backcross breeding program based on the interspecific cross of Lycopersicon hirsutum and L. esculentum yielded stable genotypes with a high ratio of fructose to glucose (〉1.5:1) compared with the approximately equimolar ratios found in L. esculentum. Two inter-simple- sequence repeat (ISSR) DNA sequences, highly associated (20 〈LOD score 〈21) with the trait, were identified. The markers were found to be less associated with either glucose or fructose levels individually (2 〈LOD score 〈3) and were statistically unlinked to total sugars and total soluble solids (TSS). These two ISSR bands segregated in a dominant fashion and were found to be allelic to each other, one associated in coupling and the other in repulsion with the trait of high fructose to glucose ratio. Both ISSR markers were mapped to the centromeric region of tomato chromosome 4. Quantitative analysis of the identified locus, based on data from segregating F2, BC and F3 populations from the cross between genotypes having high and low fructose to glucose ratios, suggested that the L. hirsutum-derived allele (Fgr H), which increases the fructose to glucose ratio, is partially dominant. Fgr H leads to an increase in fructose levels and a subsequent decrease in glucose levels, with no effect on total hexose levels. Accordingly, we conclude that the Fgr locus modulates the partitioning of hexose sugars between fructose and glucose, with no effect on total sugars or TSS.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 68 (1984), S. 493-501 
    ISSN: 1432-2242
    Keywords: Chloroplast ; Chromoplast ; Squash ; Cucurbita-ransformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The influence of allelic state of gene B on skin pigmentation in two cultivars of Cucurbita pepo L. has been studied. Total carotenoids were lower at early stages of fruit development in cultivar (cv.) ‘Early Prolific’ (EP) BB YY fruit skin, than in EP B + B + YY fruit skin, but no differences were observed in total skin carotenoids twenty days after anthesis. Total carotenoids were lower in cv. ‘Fordhook Zucchini’ (FZ) BB yy fruit skin, than in FZ B + B + yy fruit skin at all developmental stages from anthesis to maturity. Both green and yellow tissues contained typical foliar carotenoids. The carotenoids from yellow fruit skin of both EP genotypes and of FZ BB were characterized by a low carotene: xanthophyll ratio, with a high proportion of the xanthophylls esterified to fatty acids. The xanthophylls of the yellow tissues were esterified with 12∶0, 14∶0, 16∶0 fatty acids. The carotenoids from the green fruit skin of FZ B + B + had a higher percentage of carotenes (primarily β-carotene) and a lower percentage of esterified xanthophylls. Spectral shapes of carotenoid fractions from all yellow tissues were similar and distinguishable from those of green FZ B + B + tissue. The results of these studies are discussed in terms of the genetic control of plastid transformation in Cucurbita pepo L.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    European journal of plant pathology 102 (1996), S. 45-50 
    ISSN: 1573-8469
    Keywords: acetochlor ; herbicides ; induced resistance ; sugars
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Pretreatment of soil with the herbicide acetochlor at 0.1–1μg g−1 significantly decreased incidence of wilt due toFusarium oxysporum f. sp.melonis in melon seedlings. Glucose, fructose and sucrose increased in leaves of inoculated and uninoculated melon plants following acetochlor treatment. The increase in sugar levels in stems and roots was less pronounced. Light intensity affected sugar content and disease incidence. The percentage of diseased plants was significantly higher in untreated plants grown under 165μE m−2 sec−1 compared to plants grown under 300μE m−2 sec−1. Lowering light intensity resulted in reduction of levels of total sugars on the third and sixth day after inoculation. Acetochlor had little or no effect on growth rate or sporulation of the pathogen in culture. The colonization rate of diseased plant stems by the pathogen was similar in herbicide-treated and untreated plants, thus excluding the possibility that disease reduction by the herbicide is related to direct fungitoxicity.
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  • 4
  • 5
    Publication Date: 2015-06-14
    Description: Motivation: Phylogenetic algorithms have begun to see widespread use in cancer research to reconstruct processes of evolution in tumor progression. Developing reliable phylogenies for tumor data requires quantitative models of cancer evolution that include the unusual genetic mechanisms by which tumors evolve, such as chromosome abnormalities, and allow for heterogeneity between tumor types and individual patients. Previous work on inferring phylogenies of single tumors by copy number evolution assumed models of uniform rates of genomic gain and loss across different genomic sites and scales, a substantial oversimplification necessitated by a lack of algorithms and quantitative parameters for fitting to more realistic tumor evolution models. Results: We propose a framework for inferring models of tumor progression from single-cell gene copy number data, including variable rates for different gain and loss events. We propose a new algorithm for identification of most parsimonious combinations of single gene and single chromosome events. We extend it via dynamic programming to include genome duplications. We implement an expectation maximization (EM)-like method to estimate mutation-specific and tumor-specific event rates concurrently with tree reconstruction. Application of our algorithms to real cervical cancer data identifies key genomic events in disease progression consistent with prior literature. Classification experiments on cervical and tongue cancer datasets lead to improved prediction accuracy for the metastasis of primary cervical cancers and for tongue cancer survival. Availability and implementation: Our software (FISHtrees) and two datasets are available at ftp://ftp.ncbi.nlm.nih.gov/pub/FISHtrees . Contact: russells@andrew.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2014-10-17
    Description: The Dominant White locus ( W ) in the domestic cat demonstrates pleiotropic effects exhibiting complete penetrance for absence of coat pigmentation and incomplete penetrance for deafness and iris hypopigmentation. We performed linkage analysis using a pedigree segregating White to identify KIT (Chr. B1) as the feline W locus. Segregation and sequence analysis of the KIT gene in two pedigrees (P1 and P2) revealed the remarkable retrotransposition and evolution of a feline endogenous retrovirus (FERV1) as responsible for two distinct phenotypes of the W locus, Dominant White, and white spotting. A full-length (7125 bp) FERV1 element is associated with white spotting, whereas a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals. For purposes of statistical analysis, the alternatives of wild-type sequence, FERV1 element, and LTR-only define a triallelic marker. Taking into account pedigree relationships, deafness is genetically linked and associated with this marker; estimated P values for association are in the range of 0.007 to 0.10. The retrotransposition interrupts a DNAase I hypersensitive site in KIT intron 1 that is highly conserved across mammals and was previously demonstrated to regulate temporal and tissue-specific expression of KIT in murine hematopoietic and melanocytic cells. A large-population genetic survey of cats ( n = 270), representing 30 cat breeds, supports our findings and demonstrates statistical significance of the FERV1 LTR and full-length element with Dominant White/blue iris ( P 〈 0.0001) and white spotting ( P 〈 0.0001), respectively.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 7
    Publication Date: 2014-11-12
    Description: While individual non-B DNA structures have been shown to impact gene expression, their broad regulatory role remains elusive. We utilized genomic variants and expression quantitative trait loci (eQTL) data to analyze genome-wide variation propensities of potential non-B DNA regions and their relation to gene expression. Independent of genomic location, these regions were enriched in nucleotide variants. Our results are consistent with previously observed mutagenic properties of these regions and counter a previous study concluding that G-quadruplex regions have a reduced frequency of variants. While such mutagenicity might undermine functionality of these elements, we identified in potential non-B DNA regions a signature of negative selection. Yet, we found a depletion of eQTL-associated variants in potential non-B DNA regions, opposite to what might be expected from their proposed regulatory role. However, we also observed that genes downstream of potential non-B DNA regions showed higher expression variation between individuals. This coupling between mutagenicity and tolerance for expression variability of downstream genes may be a result of evolutionary adaptation, which allows reconciling mutagenicity of non-B DNA structures with their location in functionally important regions and their potential regulatory role.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2013-06-24
    Description: Motivation: Development and progression of solid tumors can be attributed to a process of mutations, which typically includes changes in the number of copies of genes or genomic regions. Although comparisons of cells within single tumors show extensive heterogeneity, recurring features of their evolutionary process may be discerned by comparing multiple regions or cells of a tumor. A useful source of data for studying likely progression of individual tumors is fluorescence in situ hybridization (FISH), which allows one to count copy numbers of several genes in hundreds of single cells. Novel algorithms for interpreting such data phylogenetically are needed, however, to reconstruct likely evolutionary trajectories from states of single cells and facilitate analysis of tumor evolution. Results: In this article, we develop phylogenetic methods to infer likely models of tumor progression using FISH copy number data and apply them to a study of FISH data from two cancer types. Statistical analyses of topological characteristics of the tree-based model provide insights into likely tumor progression pathways consistent with the prior literature. Furthermore, tree statistics from the resulting phylogenies can be used as features for prediction methods. This results in improved accuracy, relative to unstructured gene copy number data, at predicting tumor state and future metastasis. Availability: Source code for software that does FISH tree building (FISHtrees) and the data on cervical and breast cancer examined here are available at ftp://ftp.ncbi.nlm.nih.gov/pub/FISHtrees. Contact: sachowdh@andrew.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 9
    Publication Date: 2005-11-15
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
    Publication Date: 2004-12-21
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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