GENE SET TESTING TO CHARACTERIZE MULTIVARIATELY DIFFERENTIALLY EXPRESSED GENES

In a gene expression experiment (using oligo array, RNA-Seq, or other platform), researchers typically seek to characterize di erentially expressed genes based on common gene function or pathway involve-ment. The eld of gene set testing provides numerous characterization methods, some of which have proven to be more valid and powerful than others. These existing gene set testing methods focus on experimental designs where there is a single null hypothesis (usually involving association with a continuous or categorical phenotype) for each gene. Increasingly common experimental designs lead to multiple null hypotheses for each gene, and the characterization of these multivariately di erentially expressed genes is of great interest. We explore extensions of existing gene set testing methods to achieve this characterization, with application to a RNA-Seq study in livestock cloning

A Shortcut for Multiple Testing on the Directed Acyclic Graph of Gene Ontology

Background: Gene set testing has become an important analysis technique in high throughput microarray and next generation sequencing studies for uncovering patterns of differential expression of various biological processes. Often, the large number of gene sets that are tested simultaneously require some sort of multiplicity correction to account for the multiplicity effect. This work provides a substantial computational improvement to an existing familywise error rate controlling multiplicity approach (the Focus Level method) for gene set testing in high throughput microarray and next generation sequencing studies using Gene Ontology graphs, which we call the Short Focus Level. Results: The Short Focus Level procedure, which performs a shortcut of the full Focus Level procedure, is achieved by extending the reach of graphical weighted Bonferroni testing to closed testing situations where restricted hypotheses are present, such as in the Gene Ontology graphs. The Short Focus Level multiplicity adjustment can perform the full top-down approach of the original Focus Level procedure, overcoming a significant disadvantage of the otherwise powerful Focus Level multiplicity adjustment. The computational and power differences of the Short Focus Level procedure as compared to the original Focus Level procedure are demonstrated both through simulation and using real data. Conclusions: The Short Focus Level procedure shows a significant increase in computation speed over the original Focus Level procedure (as much as ∼15,000 times faster). The Short Focus Level should be used in place of the Focus Level procedure whenever the logical assumptions of the Gene Ontology graph structure are appropriate for the study objectives and when either no a priori focus level of interest can be specified or the focus level is selected at a higher level of the graph, where the Focus Level procedure is computationally intractable

Statistical Methods for Assessing Individual Oocyte Viability Through Gene Expression Profiles

In vivo derived oocytes are held as the gold standard for viability, other known origination methods are sub-par by comparison. Due to the low-viability of oocytes originating from these alternate methods, research was conducted to determine and quantify the validity of these alternate origination methods. However, the larger question of viability is on the individual oocyte level. We propose and compare methods of measurement based on gene expression profiles (GEPs) in order to assess oocyte viability, independent of oocyte origin. The first is based on a previously published wRMSD quantification of GEP differences. We also consider three novel methods: a distance comparison method, a tolerance interval method, and a classification-tree decision method; each utilizes a variable selection technique that focuses on the most differentially expressed genes. In our project, we obtain GEPs of individual swine oocytes and a general GEP distribution for in vivo oocytes. This distribution was the comparison standard for all oocytes, to gain a classification of viability. Each method is a valid method for driving viability decisions of the individual oocytes

Pasture Management to Improve Dry Matter Intake

Agricultural producers are constantly looking for ways to maximize returns while reducing input costs. On dairy operations, a move from confinement feeding to pasture grazing offers the potential to reduce costs associated with harvest and storage of feed. In such a transition, producers sometimes report a decline in milk production and growth of livestock—both of which can strongly correlate to dry matter intake. Fortunately, dry matter intake is something that can be influenced by management practices. In this publication, we discuss the pasture management practices to improve dry matter intake

Effects of electrical biostimulation and silver ions on porcine fibroblast cells.

The medical applications of electrical biostimulation and silver ions have been evaluated in laboratory experiments and clinical studies for more than two decades. Their effects on preventing infection and promoting wound healing have been described. However, little is known about the role of electrical biostimulation and/or silver ion on changes in cellular transcriptome dynamics. To our knowledge, few studies have been conducted to investigate the potential of electrical biostimulation and silver ions in cell reprogramming. Besides, it is essential to assess any possible adverse effects or potential benefits of the silver ions on mammalian cells to address its safety concerns and to improve silver medical products. In this study, we investigated transcriptomic changes in porcine fibroblast cells in response to electrical biostimulation in the presence of silver ions. Exposed cells presented distinct morphological changes after treatment, which was mainly due to the exposure of silver ions rather than the electrical current itself. Gene expression analyses suggested that electrical biostimulation and silver ions did not increase the expression of pluripotency genes. Interestingly, a set of genes related to cellular metabolic processes were differentially expressed after cells were exposed to electrically generated silver ions for 21 hours. We found that 2.00 mg/L of electrically generated silver ion caused an increase of ATP generation and an increase of the total pool of NAD+ and NADH, while ROS production did not change. Aside from toxic effects, the results reported herein demonstrate the alternative effects of silver ions on mammalian cells, especially an oxidative phosphorylation burst. To our knowledge, this response of mammalian cells to silver ions has not been described previously. Although the function of this burst is not understood, it may lead to alterations in cellular activities such as metabolic remodeling and cell reprogramming, and/or serve an as-yet unknown function in neutralization or detoxification of the silver ions within the cells

Evaluation of Commerical Ultra Narrow Cotton Production in Arizona

Seven commercial ultra narrow row (UNR) cotton fields were monitored on a weekly basis in Maricopa County, AZ in 1999. Varieties of Delta Pine and Sure Grow were planted from April 15 to June 1 and reached cut-out after accumulating 1913 to 2327 heat units after planting. Average yield for UNR cotton was 2.1 bales per acre which was 0.4 bales per acre lower than the five year average for cotton planted on conventional row spacings. Fiber quality from gin records for 801 bales had average micronaire readings of 4.54 and grades of 11 and 21 for 74% of bales. Discounts for extraneous matter (bark, grass, and cracked seed) was 5.4% and average strength (34.8) and staple lengths (27.12) were in acceptable ranges. Total cash costs ranged from $450 to$705

Porcine Skin-Derived Progenitor (SKP) Spheres and Neurospheres: Distinct “Stemness” Identified by Microarray Analysis

Skin-derived progenitors (SKP) are neural crest derived and can generate neural and mesodermal progeny in vitro, corresponding to the multipotency of neural crest stem cells. Likewise, neural stem/progenitor cells (displaying as neurospheres) have the capacity of self-renewing, and can produce most phenotypes in the nervous system. Both form spheres when cultured with epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF). Although the “stemness” of neural stem/progenitor cells has been extensively investigated, the molecular comparison of SKP spheres and neurospheres has not been elucidated. Here, SKP spheres and neurospheres from the same individual porcine fetuses were isolated with the same culture medium, and the multipotency was tested by in vitro differentiation assays. Microarray analysis was used to illustrate the “stemness” of SKP spheres and neurospheres. The upregulated genes that were in common in the SKP spheres and neurospheres are involved in ribosome, tight junction, gap junction, cell communication, calcium signaling, ErbB signaling, JAK–STAT signaling, MAPK signaling, etc. The differentially expressed genes between SKP spheres and neurospheres are mainly involved in ECM–receptor interaction and the transforming growth factor-beta (TGF-β) signaling pathway. Finally, treatment with leukemia inhibitory factor (LIF) or MEK inhibitor results in a distinctive impact on the “stemness” and differentiation genes of SKP spheres and neurospheres. Thus, the cell-intrinsic genetic program may contribute to the innate “stemness” of SKP spheres and neurospheres in a similar local microenvironment