Network analyses reveal shifts in transcript profiles and metabolites that accompany the expression of sun and an elongated tomato fruit

SUN controls elongated tomato (Solanum lycopersicum) shape early in fruit development through changes in cell number along the different axes of growth. The gene encodes a member of the IQ domain family characterized by a calmodulin binding motif. To gain insights into the role of SUN in regulating organ shape, we characterized genome-wide transcriptional changes and metabolite and hormone accumulation after pollination and fertilization in wild-type and SUN fruit tissues. Pericarp, seed/placenta, and columella tissues were collected at 4, 7, and 10 d post anthesis. Pairwise comparisons between SUN and the wild type identified 3,154 significant differentially expressed genes that cluster in distinct gene regulatory networks. Gene regulatory networks that were enriched for cell division, calcium/transport, lipid/hormone, cell wall, secondary metabolism, and patterning processes contributed to profound shifts in gene expression in the different fruit tissues as a consequence of high expression of SUN. Promoter motif searches identified putative cis-elements recognized by known transcription factors and motifs related to mitotic-specific activator sequences. Hormone levels did not change dramatically, but some metabolite levels were significantly altered, namely participants in glycolysis and the tricarboxylic acid cycle. Also, hormone and primary metabolite networks shifted in SUN compared with wild-type fruit. Our findings imply that SUN indirectly leads to changes in gene expression, most strongly those involved in cell division, cell wall, and patterningrelated processes. When evaluating global coregulation in SUN fruit, the main node represented genes involved in calcium-regulated processes, suggesting that SUN and its calmodulin binding domain impact fruit shape through calcium signaling.Fil: Clevenger, Josh P..Fil: Van Houten, Jason.Fil: Blackwood, Michelle.Fil: Rodríguez, Gustavo Rubén. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Jikumaru, Yusuke.Fil: Kamiya, Yuji.Fil: Kusano, Miyako.Fil: Saito, Kazuki.Fil: Visa, Sofia.Fil: Van Der Knaap, Esther

Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America

The process of plant domestication is often protracted, involving underexplored intermediate stages with important implications for the evolutionary trajectories of domestication traits. Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. to a semidomesticated intermediate, S. lycopersicum L. var. cerasiforme (SLC) in South America, and a second transition from SLC to fully domesticated S. lycopersicum L. var. lycopersicum in Mesoamerica. In this study, we employ population genomic methods to reconstruct tomato domestication history, focusing on the evolutionary changes occurring in the intermediate stages. Our results suggest that the origin of SLC may predate domestication, and that many traits considered typical of cultivated tomatoes arose in South American SLC, but were lost or diminished once these partially domesticated forms spread northward. These traits were then likely reselected in a convergent fashion in the common cultivated tomato, prior to its expansion around the world. Based on these findings, we reveal complexities in the intermediate stage of tomato domestication and provide insight on trajectories of genes and phenotypes involved in tomato domestication syndrome. Our results also allow us to identify underexplored germplasm that harbors useful alleles for crop improvement

The Effect of Class Imbalance, Complexity, Size, and Learning Distribution on Classifier Performance

Classes of real world datasets have various properties (such as imbalance, size, complexity, and class distribution) that make the classification task more difficult. We investigate the robustness of six classification techniques over data having various combinations of the above mentioned properties. One artificial domain and six real world datasets are used in these experiments. Results of our analysis point to the frequency-based classifiers (such as the fuzzy and the Bayes classifiers) as being more robust over various imbalance, size, complexity, and training distribution. © 2011 Inderscience Enterprises Ltd

Issues in mining imbalanced data sets - a review paper

This paper traces some of the recent progress in the field of learning of imbalanced data. It reviews approaches adopted for this problem and it identifies challenges and points out future directions in this relatively new field

2004a. Experiments in guided class rebalance based on class structure

Up-sampling and down-sampling are the two most used methods in balancing the data when dealing with two class imbalance problem. However, none of the existing approaches to class rebalance take into account class information (e.g. distribution, within and between class distances, imbalance factor). This study presents initial results of up-sampling methods based on various approaches to aggregation of class information such as spread, imbalance factor and the distance between the classes. Artificially generated data are used for experiments. The performance of each up-sampling method is evaluated with respect to how well the resulting data set reflects the underlying original class distribution, in terms of mean, standard deviation and (empirical) distribution function

Fuzzy Classifiers - Opportunities and Challenges

Several issues arise when we consider building classifiers in general, and fuzzy classifiers in particular. These issues include but are not limited to attribute/feature selection, adoption of a specific approach/algorithm, evaluate the classifier performance, etc. We consider the opportunities that such classifiers have to offer and contrast them with the challenges they pose. © 2011 Springer-Verlag

A Stochastic Treatment of Similarity

This study investigates a robust measure of similarity applicable in many domains and across many dimensions of data. Given a distance or discrepancy measure on a domain, the similarity of two values in this domain is defined as the probability that any pair of values from that domain are more different (at a larger distance) than these two values are. We discuss the motivation for this approach, its properties, and the issues that arise from it. © 2010 Springer-Verlag Berlin Heidelberg

Coincidental Collaborations: Bridging Communities of Practice on the Liberal Arts Campus

This presentation offers perspectives from the College of Wooster’s Computer Science and Library faculties on the development of a project that will ultimately result in digital editions of Madeleine de Scudéry’s series of seventeenth- and eighteenth-century _Conversations_. French Professor Laura Burch, after teaching from PDF copies of seventeenth-century books, noted that students had as many difficulties with the printed typography as with the antiquated French. A project developed in which students transcribed, but did not modernize, the text. Working with Emerging Technologies Librarian Stephen Flynn, who will speak for the project, this team produced a TEI-encoded copy of the first volume of _Conversations_, _Conversations Sur Divers Sujets_ (1680). Flynn will discuss the project’s workflow, which included a low-barrier version of XML that made encoding easier for the students while allowing for transformations into TEI once transcriptions were completed. A partner project arose from this in which CS Professor Sofia Visa guided a research project by CS student Will Rial, both of whom will present on their experiences. Rial used Machine Learning and Optical Character Recognition (OCR) technologies to automate the transcription of the first volume of _Conversations_ as a pilot for processing the remaining four volumes. Rial will discuss his optimization of the workflows developed in the Early Modern OCR Project (eMOP), including dictionary creation and post-processing algorithms, and Visa will present on the pedagogical perspective of guiding such a project

Rider Transposon Insertion and Phenotypic Change in Tomato

The Rider retrotransposon is ubiquitous in the tomato genome and is likely an autonomous element that still transposes to date. The majority of approximately 2,000 copies of Rider are located near genes. Phenotypes associated with Rider insertion are diverse and often the result of knock out of the underlying genes. One unusual Rider-mediated phenotype resulted from a gene duplication event. By means of read-through transcription, Rider copied part of the surrounding sequence to another location in the genome, leading to high expression of one of the transposed genes, SUN, resulting in an elongated fruit shape. Transcription studies demonstrated that Rider is expressed to levels comparable to the expression of other tomato genes and that control of transposition may be regulated by antisense transcription. Taken together, Rider is a unique retrotransposon that may have played important roles in the evolution of tomato and its closest relatives. © Springer-Verlag Berlin Heidelberg 2012