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Full-Text Articles in Life Sciences

Nonsyntenic Genes Drive Highly Dynamic Complementation Of Gene Expression In Maize Hybrids, Anja Paschold, Nick B. Larson, Caroline Marcon, James C. Schnable, Cheng-Ting Yeh, Christa Lanz, Dan Nettleton, Hans-Peter Piepho, Patrick S. Schnable, Frank Hochholdinger Oct 2014

Nonsyntenic Genes Drive Highly Dynamic Complementation Of Gene Expression In Maize Hybrids, Anja Paschold, Nick B. Larson, Caroline Marcon, James C. Schnable, Cheng-Ting Yeh, Christa Lanz, Dan Nettleton, Hans-Peter Piepho, Patrick S. Schnable, Frank Hochholdinger

Statistics Publications

Maize (Zea mays) displays an exceptional level of structural genomic diversity, which is likely unique among higher eukaryotes. In this study, we surveyed how the genetic divergence of two maize inbred lines affects the transcriptomic landscape in four different primary root tissues of their F1-hybrid progeny. An extreme instance of complementation was frequently observed: genes that were expressed in only one parent but in both reciprocal hybrids. This single-parent expression (SPE) pattern was detected for 2341 genes with up to 1287 SPE patterns per tissue. As a consequence, the number of active genes in hybrids exceeded that of their parents ...


Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton Sep 2014

Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton

Statistics Publications

Heterosis, also known as the hybrid vigor, occurs when the mean phenotype of hybrid offspring is superior to that of its two inbred parents. The heterosis phenomenon is extensively utilized in agriculture though the molecular basis is still unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers have begun to compare expression levels of thousands of genes between parental inbred lines and their hybrid offspring to search for evidence of gene expression heterosis. Standard statistical approaches for separately analyzing expression data for each gene can produce biased and highly variable estimates and unreliable tests of heterosis ...


Parametric And Nonparametric Statistical Methods For Genomic Selection Of Traits With Additive And Epistatic Genetic Architectures, Reka Howard, Alicia L. Carriquiry, William D. Beavis Jun 2014

Parametric And Nonparametric Statistical Methods For Genomic Selection Of Traits With Additive And Epistatic Genetic Architectures, Reka Howard, Alicia L. Carriquiry, William D. Beavis

Statistics Publications

Parametric and nonparametric methods have been developed for purposes of predicting phenotypes. These methods are based on retrospective analyses of empirical data consisting of genotypic and phenotypic scores. Recent reports have indicated that parametric methods are unable to predict phenotypes of traits with known epistatic genetic architectures. Herein, we review parametric methods including least squares regression, ridge regression, Bayesian ridge regression, least absolute shrinkage and selection operator (LASSO), Bayesian LASSO, best linear unbiased prediction (BLUP), Bayes A, Bayes B, Bayes C, and Bayes Cp. We also review nonparametric methods including Nadaraya-Watson estimator, reproducing kernel Hilbert space, support vector machine regression ...


Heterogeneous Variances In Multi-Environment Yield Trials For Corn Hybrids, Massiel Andrea Orellana, Jode Edwards, Alicia L. Carriquiry Apr 2014

Heterogeneous Variances In Multi-Environment Yield Trials For Corn Hybrids, Massiel Andrea Orellana, Jode Edwards, Alicia L. Carriquiry

Statistics Publications

Recent developments in statistics and computing have enabled much greater levels of complexity in statistical models of multi-environment yield trial data. One particular feature of interest to breeders is simultaneously modeling heterogeneity of variances among environments and hybrids. Our objective was to estimate the level of heterogeneity of genotype by environment interaction variance and error variance in the Iowa Crop Performance Test for Corn. A Bayesian approach was used to estimate variance components in a hierarchical model that allows for heterogeneous error and genotypeby- environment interaction (GEI) variances applied to corn yield data from the Iowa Crop Performance Test performed ...


Review Of "A Primer Of Ecological Statistics. Second Edition", Philip M. Dixon Jan 2014

Review Of "A Primer Of Ecological Statistics. Second Edition", Philip M. Dixon

Statistics Publications

The second edition of this ecological statistics textbook adds two chapters on distinctive statistical methods used for ecological questions. One new chapter covers estimating species richness and other diversity metrics; this chapter focuses on rarefaction curves, although there is a short discussion of Chao’s estimators of assemblage richness. The second new chapter focuses on occupancy modeling with short discussions of mark-recapture models for closed and open populations. Combined with the chapter on ordination that was in the first edition, this volume now provides an introduction to the major areas of ecological statistics.


Salmonella Enterica Serovar Typhimurium-Infected Pigs With Different Shedding Levels Exhibit Distinct Clinical, Peripheral Cytokine And Transcriptomic Immune Response Phenotypes, Susan M. Knetter, Shawn M. D. Bearson, Ting-Hua Huang, Dason Kurkiewicz, Martine Schroyen, Dan Nettleton, Daniel Berman, Valerie Cohen, Joan K. Lunney, Amanda E. Ramer-Tait, Michael J. Wannemeuhler, Christopher K. Tuggle Jan 2014

Salmonella Enterica Serovar Typhimurium-Infected Pigs With Different Shedding Levels Exhibit Distinct Clinical, Peripheral Cytokine And Transcriptomic Immune Response Phenotypes, Susan M. Knetter, Shawn M. D. Bearson, Ting-Hua Huang, Dason Kurkiewicz, Martine Schroyen, Dan Nettleton, Daniel Berman, Valerie Cohen, Joan K. Lunney, Amanda E. Ramer-Tait, Michael J. Wannemeuhler, Christopher K. Tuggle

Statistics Publications

Foodborne salmonellosis costs the US $2.7 billion/year, including $100.0 million in annual losses to pork producers. Pigs colonized with Salmonella are usually asymptomatic with varied severity and duration of fecal shedding. Thus, understanding the responses that result in less shedding may provide a mechanism for control. Fifty-four pigs were inoculated with Salmonella enterica serovar Typhimurium (ST) and clinical signs, fecal ST shedding, growth performance, peripheral cytokines and whole blood gene expression were measured. Persistently shedding (PS) pigs had longer pyrexia and elevated serum IL-1β, TNF-α and IFN-γ compared with low shedding (LS) pigs, while LS pigs had ...


Copy Number Variation Detection Using Next Generation Sequencing Read Counts, Heng Wang, Dan Nettleton, Kai Ying Jan 2014

Copy Number Variation Detection Using Next Generation Sequencing Read Counts, Heng Wang, Dan Nettleton, Kai Ying

Statistics Publications

Background: A copy number variation (CNV) is a difference between genotypes in the number of copies of a genomic region. Next generation sequencing (NGS) technologies provide sensitive and accurate tools for detecting genomic variations that include CNVs. However, statistical approaches for CNV identification using NGS are limited. We propose a new methodology for detecting CNVs using NGS data. This method (henceforth denoted by m-HMM) is based on a hidden Markov model with emission probabilities that are governed by mixture distributions. We use the Expectation-Maximization (EM) algorithm to estimate the parameters in the model.

Results: A simulation study demonstrates that our ...


Student Interpretations Of Phylogenetic Trees In An Introductory Biology Course, Jonathan Dees, Jennifer L. Momsen, Jarad Niemi, Lisa Montplaisir Jan 2014

Student Interpretations Of Phylogenetic Trees In An Introductory Biology Course, Jonathan Dees, Jennifer L. Momsen, Jarad Niemi, Lisa Montplaisir

Statistics Publications

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also ...