Re-annotation of the woodland strawberry (Fragaria vesca) genome

Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1. The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae (http://www.rosaceae.org/). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results. Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.https://doi.org/10.1186/s12864-015-1221-

Vision, challenges and opportunities for a Plant Cell Atlas

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.</jats:p

A Network Approach to Identify Key Regulators of Fruit Development in Fragaria vesca, a Diploid Strawberry

Post-embryonic organogenesis is a feature unique to plants, an example of which is flower and fruit production. Previous work on strawberry fruit development has focused primarily on the latter stages, including ripening. Comparatively little is known about the molecular events underpinning fruit set, the pivotal stage at which fruit development proceeds or terminates. This thesis investigates early fruit development using Fragaria vesca, a diploid strawberry, as a model. In collaboration with a bioinformatician, I generated gene co-expression networks from 92 previously generated RNA-Seq libraries profiling multiple tissues and stages of strawberry flower and fruit development. I demonstrate the utility of co-expression networks in illuminating molecular processes underlying fruit development. Experimental validation of the networks includes demonstration of increased iron transport soon after fertilization and identification of FveUFO1 as an important regulator of floral meristem determinacy and floral organ identity. Using the co-expression networks, I discovered the surprising expression of FvFT1, a homolog of FLOWERING LOCUS T (FT), in the fleshy fruit immediately post-fertilization. In many plant species, the FT peptide is a non-cell autonomous signal that initiates flowering in response to inductive photoperiod. I found that FvFT1 expression is responsive to temperature, but not photoperiod, in strawberry fruit. Further, transcriptional activation is detectable in the vascular bundles connecting the fruit to the seeds, raising the possibility that FvFT1 may facilitate cross-tissue communication. Signal from an FvFT1-GFP translational fusion protein is visible in seed nuclei despite its localized transcription in the vasculature. However, analysis of FvFT1 RNAi plants failed to identify a fruit phenotype, possibly due to redundancy among three FvFT paralogs. Finally, to develop additional research tools for F. vesca, I isolated and tested fruit tissue-specific promoters based on genes identified with differential expression analyses. These analyses revealed genes strongly expressed in the receptacle fruit, thereby identifying potential regulators of early fruit development and attractive candidates for future study. Together, this work advances the systems-level infrastructure for studying molecular regulation of F. vesca fruit development, points to a novel role for FT distinct from its known function in floral initiation, and provides molecular tools useful to the F. vesca community

Detection of Occult Foci of Breast Cancer Using Breast-Specific Gamma Imaging in Women with One Mammographic or Clinically Suspicious Breast Lesion

Rationale and Objectives: The aim of this study was to determine how often breast-specific gamma imaging (BSGI) identifies occult cancerous lesions in women with one suspicious lesion detected on mammography or physical exam. Materials and Methods: A retrospective review was performed of the records of all patients who underwent BSGI between January 1, 2004, and June 4, 2007. Included in the study were 159 women who had one suspicious breast lesion on physical exam and/or mammography and who underwent BSGI to evaluate for occult lesions in the breast. All patients had one or more foci of cancer proven pathologically. BSGI findings were classified as normal or abnormal on the basis of the presence of focal radiotracer uptake. Results: BSGI detected additional suspicious lesions occult to mammography and physical exam in 46 of 159 women (29%). BSGI identified occult cancer in 14 of 40 women (35%) who underwent biopsy or excision because of BSGI findings and in 14 of the 159 (9%) women in this study. In nine women, the occult cancer was present in the same breast as the index lesion (6%), and in five women, the occult cancer was found in the contralateral breast (3%). Conclusions: BSGI is an effective imaging modality in the identification of mammographically and clinically occult cancer in women with one suspicious breast lesion. © 2010 AUR

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

Single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality datasets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation, and to make the data readily available to the community in this fast-developing field of research

Eosinophil-mediated signalling attenuates inflammatory responses in experimental colitis

Objective Eosinophils reside in the colonic mucosa and increase significantly during disease. Although a number of studies have suggested that eosinophils contribute to the pathogenesis of GI inflammation, the expanding scope of eosinophil-mediated activities indicate that they also regulate local immune responses and modulate tissue inflammation. We sought to define the impact of eosinophils that respond to acute phases of colitis in mice. Design Acute colitis was induced in mice by administration of dextran sulfate sodium, 2,4,6- trinitrobenzenesulfonic acid or oxazolone to C57BL/6J (control) or eosinophil deficient (PHIL) mice. Eosinophils were also depleted from mice using antibodies against interleukin (IL)-5 or by grafting bone marrow from PHIL mice into control mice. Colon tissues were collected and analysed by immunohistochemistry, flow cytometry and reverse transcription PCR; lipids were analysed by mass spectroscopy. Results Eosinophil-deficient mice developed significantly more severe colitis, and their colon tissues contained a greater number of neutrophils, than controls. This compensatory increase in neutrophils was accompanied by increased levels of the chemokines CXCL1 and CXCL2, which attract neutrophils. Lipidomic analyses of colonic tissue from eosinophil-deficient mice identified a deficiency in the docosahexaenoic acidderived anti-inflammatory mediator 10, 17- dihydroxydocosahexaenoic acid (diHDoHE), namely protectin D1 (PD1). Administration of an exogenous PD1-isomer (10S, 17S-DiHDoHE) reduced the severity of colitis in eosinophil-deficient mice. The PD1-isomer also attenuated neutrophil infiltration and reduced levels of tumour necrosis factor-α, IL-1β, IL-6 and inducible NOsynthase in colons of mice. Finally, in vitro assays identified a direct inhibitory effect of PD1-isomer on neutrophil transepithelial migration. Conclusions Eosinophils exert a protective effect in acute mouse colitis, via production of anti-inflammatory lipid mediators

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research