@article {316,
	title = {The cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation.},
	journal = {Development},
	volume = {142},
	year = {2015},
	month = {2015 Feb 15},
	pages = {712-21},
	abstract = {<p>Cyclophilin A is a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation.</p>},
	keywords = {Arabidopsis, Biological Transport, Cyclophilin A, Indoleacetic Acids, Lycopersicon esculentum, Plant Proteins, Plant Roots, Plant Shoots},
	issn = {1477-9129},
	doi = {10.1242/dev.113225},
	author = {Ivanchenko, Maria G and Zhu, Jinsheng and Wang, Bangjun and Medveck{\'a}, Eva and Du, Yunlong and Azzarello, Elisa and Mancuso, Stefano and Megraw, Molly and Filichkin, Sergei and Dubrovsky, Joseph G and Friml, Ji{\v r}{\'\i} and Geisler, Markus}
}
@article {318,
	title = {A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.},
	journal = {J Exp Bot},
	volume = {65},
	year = {2014},
	month = {2014 Nov},
	pages = {5889-902},
	abstract = {<p>Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated with physiological ripening stages and the transcriptional changes between stages within the ripening programme. In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified, mainly due to the lack of mutants for comparative transcriptomic studies. A feature in grape cluster ripening (Vitis vinifera cv. Pinot noir), where all berries do not initiate the ripening at the same time, was exploited to study their shifted ripening programmes in parallel. Berries that showed marked ripening state differences in a v{\'e}raison-stage cluster (ripening onset) ultimately reached similar ripeness states toward maturity, indicating the flexibility of the ripening programme. The expression variance between these v{\'e}raison-stage berry classes, where 11\% of the genes were found to be differentially expressed, was reduced significantly toward maturity, resulting in the synchronization of their transcriptional states. Defined quantitative expression changes (transcriptional distances) not only existed between the v{\'e}raison transitional stages, but also between the v{\'e}raison to maturity stages, regardless of the berry class. It was observed that lagging berries complete their transcriptional programme in a shorter time through altered gene expressions and ripening-related hormone dynamics, and enhance the rate of physiological ripening progression. Finally, the reduction in expression variance of genes can identify new genes directly associated with ripening and also assess the relevance of gene activity to the phase of the ripening programme.</p>},
	keywords = {Fruit, Gene Expression Profiling, Gene Expression Regulation, Plant, Oligonucleotide Array Sequence Analysis, Plant Growth Regulators, Time Factors, Transcription, Genetic, Vitis},
	issn = {1460-2431},
	doi = {10.1093/jxb/eru329},
	author = {Gouthu, Satyanarayana and O{\textquoteright}Neil, Shawn T and Di, Yanming and Ansarolia, Mitra and Megraw, Molly and Deluc, Laurent G}
}
