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Table of contents
- Introduction
- YEATS domain-containing protein 4
- Applications of Supercomputers in Sequence Analysis and Genome Annotation
- Subtropolis Film Partners, Turning Point Ministries - Alignable
Background was corrected by the robust multi-array average RMA method. Differentially expressed genes were extracted using the Bioconductor Microarray Significant Profiles MaSigPro R package for the analysis of single and multiseries time course microarray experiments [ 51 ]. MaSigPro follows a two step regression strategy to find genes with significant temporal expression changes and significant differences between experimental groups. The method defined a general regression model for the data. Second, a variable selection procedure was applied to find significant variables for each gene, for which a stepwise regression was employed step.
Genes whose expression did not change were excluded to minimize background noise. Gene clustering was also performed using the k -means method [ 83 ] with Pearson correlation distances. The same RNA samples hybridised to the microarray were used for this purpose. From analysis of the data with geNorm and BestKeeper software [ 85 , 86 ], CmCYP7 was found to be the most stable reference gene and used as the reference in all samples, as in previous experiments [ 47 , 87 ].
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Intra-assay variation was evaluated by performing all amplification reactions in triplicate. The specificity of the PCR amplification was checked in preliminary experiments by electrophoresis on an Agilent Bioanalyzer Agilent Technologies , and routinely in the main experiments by melting curve analysis and agarose gel electrophoresis.
The relative expression of target genes was calculated using Cp values calculated by LC software and equation 1 :. Since the efficiency of amplification E was between 0.
Introduction
Data were transformed to a log 2 scale to make the data comparable with the microarray results. Genes that were differentially expressed during fruit ripening in Ved and PS were identified by analysis of the microarray data using the Significance Analysis of Microarrays SAM algorithm in the TM4 software package [ 91 ], and by analysis with the Robin software package [ 67 ].
Data were displayed using MapMan [ 68 ]. Treatment of fruit with propylene gives information about the biogenesis of ethylene. Giovannoni JJ. Genetic regulation of fruit development and ripening. Plant Cell. Quality of cantaloupe muskmelons: Variability and attributes. Scientia Hort. Biochemistry of fruit ripening.
Post-harvest physiology of climacteric fruits: recent developments in the biosynthesis and action of ethylene. Sci Aliments. Utilization of tomato microarrays for comparative gene expression analysis in the Solanaceae. J Exp Bot. Fruit ripening mutants yield insights into ripening control. Curr Opin Plant Biol. Plant J. Ethylene signalling and response: where different regulatory modules meet. Curr Opin Plant Sci. Alexander L, Grierson D. Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening.
Klee HJ. Ethylene signal transduction. Moving beyond Arabidopsis. Plant Physiol.
YEATS domain-containing protein 4
Signal transduction systems regulating fruit ripening. Trends Plant Sci. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor rin locus. NOR gene compositions and methods for use thereof. July 13, A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening.
Nat Genet. Regulation of ripening and opportunities for control in tomato and other fruits. Plant Biotechnol J. Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet. Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses. Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato.
Mol Genet Genom. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol. Identification of mRNAs with enhanced expression in ripening strawberry fruit using polymerase chain reaction differential display.
Applications of Supercomputers in Sequence Analysis and Genome Annotation
Plant Mol Biol. Manning K. Isolation of a set of ripening-related genes from strawberry: Their identification and possible relationship to fruit quality traits. Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior. Ezura H, Owino WO. Melon ripening and ethylene.
Plant Sci. Climacteric fruit ripening: ethylene-dependent and independent regulation of ripening pathways in melon fruit. Interaction between QTLs induces an advance in ethylene biosynthesis during melon fruit ripening. Theor Appl Genet. Ethylene production, respiration, and internal gas concentrations in cantaloupe fruits at various stages of maturity.
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Characterization of ripening-regulated cDNAs and their expression in ethylene-suppressed Charentais melon fruit. Expression of ACC oxidase antisense gene inhibits ripening of cantaloupe melon fruits. Identification of quantitative trait loci involved in fruit quality traits in melon Cucumis melo L. A consensus linkage map identifies genomic regions controlling fruit maturity and beta-carotene-associated flesh color in melon Cucumis melo L.
Metabolic and molecular events occurring during chromoplast biogenesis. J Bot. Fruit growth and development, ripening, and role of ethylene in honey dew muskmelon. J Am Soc Hortic Sci. Physiological-changes during development and ripening of perlita muskmelon fruits. Sci Hortic.