Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray

US National Institutes of Health [1R15GM07719201A1]; US National Science Foundation [IOS-0817818]; Ohio Plant Biotech Consortium; National Natural Science Foundation of China [60774033]; Specialized Research Fund for the Doctoral Program of Higher EducatiBackground: Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development and in flowering time control. The function of PCFS4 in controlling flowering time was correlated with the alternative polyadenylation of FCA, a flowering time regulator. However, genetic evidence suggested additional targets of PCFS4 that may mediate its function in both flowering time and leaf development. Methodology/Principal Findings: To identify further targets, we investigated the whole transcriptome of a PCFS4 mutant using Affymetrix Arabidopsis genomic tiling 1.0R array and developed a data analysis pipeline, termed RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression). In RADPRE, ratios of normalized probe intensities between wild type Columbia and a pcfs4 mutant were first generated. By doing so, one of the major problems of tiling array data-variations caused by differential probe affinity-was significantly alleviated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Col/pcfs4 and pcfs4/Col ratios as inputs. Gene Ontology (GO) analysis of the DPGs and DEGs revealed potential new roles of PCFS4 in stress responses besides flowering time regulation. Conclusion/Significance: We identified 68 DPGs and 114 DEGs with FDR at 1% and 2%, respectively. Most of the 68 DPGs were subjected to alternative polyadenylation, splicing or transcription initiation. Quantitative PCR analysis of a set of DPGs confirmed that most of these genes were truly differentially processed in pcfs4 mutant plants. The enriched GO term "regulation of flower development'' among PCFS4 targets further indicated the efficacy of the RADPRE pipeline. This simple but effective program is available upon request

Forecasting and Operational Research:A Review

From its foundation, operational research (OR) has made many substantial contributions to practical forecasting in organizations. Equally, researchers in other disciplines have influenced forecasting practice. Since the last survey articles in JORS, forecasting has developed as a discipline with its own journals. While the effect of this increased specialization has been a narrowing of the scope of OR's interest in forecasting, research from an OR perspective remains vigorous. OR has been more receptive than other disciplines to the specialist research published in the forecasting journals, capitalizing on some of their key findings. In this paper, we identify the particular topics of OR interest over the past 25 years. After a brief summary of the current research in forecasting methods, we examine those topic areas that have grabbed the attention of OR researchers: computationally intensive methods and applications in operations and marketing. Applications in operations have proved particularly important, including the management of inventories and the effects of sharing forecast information across the supply chain. The second area of application is marketing, including customer relationship management using data mining and computer-intensive methods. The paper concludes by arguing that the unique contribution that OR can continue to make to forecasting is through developing models that link the effectiveness of new forecasting methods to the organizational context in which the models will be applied. The benefits of examining the system rather than its separate components are likely to be substantial

Morphological alterations induced by doxorubicin on H9c2 myoblasts: nuclear, mitochondrial, and cytoskeletal targets

Abstract Doxorubicin (Dox) is a very potent antineoplastic agent used against several types of cancer, despite a cumulative cardiomyopathy that reduces the therapeutic index for treatment. H9c2 myoblast cells have been used as an in vitro model to study biochemical alterations induced by Dox treatment on cardiomyocyte cells. Despite the extensive work already published, few data are available regarding morphological alterations of H9c2 cells during Dox treatment. The purpose of the present work was to evaluate Dox-induced morphological alterations in H9c2 myoblasts, focusing especially on the nuclei, mitochondria, and structural fibrous proteins. Treatment of H9c2 cell with low concentrations of Dox causes alterations in fibrous structural proteins including the nuclear lamina and sarcomeric cardiac myosin, as well as mitochondrial depolarization and fragmentation, membrane blebbing with cell shape changes, and phosphatidylserine externalization. For higher Dox concentrations, more profound alterations are evident, including nuclear swelling with disruption of nuclear membrane structure, mitochondrial swelling, and extensive cytoplasm vacuolization. The results obtained indicate that Dox causes morphological alterations in mitochondrial, nuclear, and fibrous protein structures in H9c2 cells, which are dependent on the drug concentration. Data obtained with the present study allow for a better characterization of the effects of Dox on H9c2 myoblasts, used as a model to study Dox-induced cardiotoxicity. The results obtained also provide new and previously unknown targets that can contribute to understand the mechanisms involved in the cardiotoxicity of Dox