First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.).

Background: Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species.

Genome-scale examination of NBS-encoding genes in blueberry.

Blueberry is an important crop worldwide. It is, however, susceptible to a variety of diseases, which can lead to losses in yield and fruit quality. Although screening studies have identified resistant germplasm for some important diseases, still little is known about the molecular basis underlying that resistance.

Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling.

Background: Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more recent Next Generation Sequencing technologies, such as RNA-Seq. In any case, information from microarrays is truthful and robust, thus it can be exploited through the integration of microarray data with RNA-Seq data.

Design and Sampling Plan Optimization for RT-qPCR Experiments in Plants: A Case Study in Blueberry.

The qPCR assay has become a routine technology in plant biotechnology and agricultural research. It is unlikely to be technically improved, but there are still challenges which center around minimizing the variability in results and transparency when reporting technical data in support of the conclusions of a study. There are a number of aspects of the pre- and post-assay workflow that contribute to variability of results.

Expression Profile of Carotenoid Cleavage Dioxygenase Genes in Summer Squash (Cucurbita pepo L.).

Carotenoids are important dietary components that can be found in vegetable crops. The accumulation of these compounds in fruit and vegetables is altered by the activity of carotenoid cleavage dioxygenases (CCDs) enzymes that produce their degradation. The aim of this work was to study the possible implication of CCD genes in preventing carotenoid storage in the horticultural crop summer squash (Cucurbita pepo L.

First TILLING platform in Cucurbita pepo: a new mutant resource for gene function and crop improvement.

Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations.

Identification of Risk Factors for the Occurrence of Cement Leakage During Percutaneous Vertebroplasty for Painful Osteoporotic or Malignant Vertebral Fracture.

Study Design: Retrospective study.

Objective: To identify fracture morphology-dependent risk factors for the occurrence of cement leakage during percutaneous vertebroplasty.

Summary Of Background Data: Extravertebral cement leakage is the most frequently reported complication and represents a major risk after vertebroplasty and balloon kyphoplasty.

Carotenogenic gene expression and carotenoid accumulation in three varieties of Cucurbita pepo during fruit development.

The control of gene expression is a crucial regulatory mechanism in carotenoid accumulation of fruits and flowers. We investigated the role of transcriptional regulation of nine genes involved in the carotenoid biosynthesis pathway in three varieties of Cucurbita pepo with evident differences in fruit color. The transcriptional levels of the key genes involved in the carotenoid biosynthesis were higher in flower-, leaf-, and fruit skin tissues than flesh tissues.

In-house validation of a multiplex real-time PCR method for simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes.

A wide variety of qPCR methods currently exist for Salmonella spp., Escherichia coli O157 and Listeria monocytogenes detection. These methods target several genes and use different detection chemistries, either in simplex or in multiplex formats.

RNA quality assessment: a view from plant qPCR studies.

Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) is probably the most common molecular technique used in transcriptome analyses today. The simplicity of the technology and associated protocols that generate results without the need to understand the underlying principles has made RT-qPCR the method of choice for RNA quantification. Rather than the 'gold standard technology' often used to describe it, the performance of RT-qPCR suffers from considerable pitfalls during general workflow.

Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding.

Introduction: Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent.

Objective: To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA.

Characterization of the 3':5' ratio for reliable determination of RNA quality.

Determination of RNA quality is a critical first step in obtaining meaningful gene expression data. The PCR-based 3':5' assay is an RNA quality assessment tool. This assay is a simple, fast, and low-cost method of selecting samples for further analysis.

Selection of reference genes for gene expression studies in zucchini (Cucurbita pepo) using qPCR.

The zucchini (Cucurbita pepo) is an important food crop, the transcriptomics of which are a fundamental tool to accelerate the development of new varieties by breeders. However, the suitability of reference genes for data normalization in zucchini has not yet been studied. The aim of this study was to assess the suitability of 13 genes for their potential use as reference genes in quantitative real-time PCR.

Evaluation of candidate reference genes for expression studies in Pisum sativum under different experimental conditions.

Reverse transcription quantitative real-time polymerase chain reaction is the most accurate measure of gene expression in biological systems. The data are analyzed through a process called normalization. Internal standards are essential for determining the relative gene expression in different samples.

Validation of QTLs for Orobanche crenata resistance in faba bean (Vicia faba L.) across environments and generations.

Broomrape (Orobanche crenata Forsk.) is a major root-parasite of faba bean (Vicia faba L.), that seriously limits crop cultivation in the whole Mediterranean area.

Gene expression analysis of molecular mechanisms of defense induced in Medicago truncatula parasitized by Orobanche crenata.

The infection of Medicago truncatula Gaertn. roots with the obligate parasite Orobanche crenata Forsk. is a useful model for studying the molecular events involved in the legumes-parasite interaction.

Variation Among and Within Populations of the Parasitic Weed Orobanche crenata from Spain and Israel Revealed by Inter Simple Sequence Repeat Markers.

ABSTRACT The patterns of genetic variation among Orobanche crenata populations from Spain and Israel were studied using radiolabeled inter simple sequence repeat amplification products that were separated in sequencing polyacrylamide gels. The analysis of molecular variance indicated that most of the genetic diversity was attributable to differences among individuals within a population although significant divergences were found between regions. The Jaccard's similarity matrix was analyzed by unweighted pair-group method with arithmetic average and the resultant dendrogram clearly divided six populations by region, with the Spanish populations being more similar to each other than the Israeli populations.

Mapping of quantitative trait loci controlling broomrape (Orobanche crenata Forsk.) resistance in faba bean (Vicia faba L.).

Orobanche crenata Forsk. is a root parasite that produces devastating effects on many crop legumes and has become a limiting factor for faba bean production in the Mediterranean region. The efficacy of available control methods is minimal and breeding for broomrape resistance remains the most promising method of control.