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Search Results: 1 - 10 of 8014 matches for " Dan Nettleton "
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The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data
Steven P. Lund,Dan Nettleton
Statistics , 2012, DOI: 10.1214/12-AOAS535
Abstract: When analyzing microarray data, hierarchical models are often used to share information across genes when estimating means and variances or identifying differential expression. Many methods utilize some form of the two-level hierarchical model structure suggested by Kendziorski et al. [Stat. Med. (2003) 22 3899-3914] in which the first level describes the distribution of latent mean expression levels among genes and among differentially expressed treatments within a gene. The second level describes the conditional distribution, given a latent mean, of repeated observations for a single gene and treatment. Many of these models, including those used in Kendziorski's et al. [Stat. Med. (2003) 22 3899-3914] EBarrays package, assume that expression level changes due to treatment effects have the same distribution as expression level changes from gene to gene. We present empirical evidence that this assumption is often inadequate and propose three-level hierarchical models as extensions to the two-level log-normal based EBarrays models to address this inadequacy. We demonstrate that use of our three-level models dramatically changes analysis results for a variety of microarray data sets and verify the validity and improved performance of our suggested method in a series of simulation studies. We also illustrate the importance of accounting for the uncertainty of gene-specific error variance estimates when using hierarchical models to identify differentially expressed genes.
Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa
Xuehui Li, Yanling Wei, Dan Nettleton, E Charles Brummer
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-107
Abstract: We tested these hypotheses in three Medicago sativa (alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix M. truncatula GeneChip arrays. Alfalfa hybridized to approximately 47% of the M. truncatula probe sets. Probe set signal intensities were analyzed using MicroArray Suite v.5.0 (MAS) and robust multi-array average (RMA) algorithms. Based on MAS analysis, the two heterotic hybrids performed similarly, with about 27% of genes showing differential expression among the parents and their hybrid compared to 12.5% for the non-heterotic hybrid. At a false discovery rate of 0.15, 4.7% of differentially expressed genes in hybrids (~300 genes) showed nonadditive expression compared to only 0.5% (16 genes) in the non-heterotic hybrid. Of the nonadditively expressed genes, approximately 50% showed expression levels that fell outside the parental range in heterotic hybrids, but only one of 16 showed a similar profile in the non-heterotic hybrid. Genes whose expression differed in the parents were three times more likely to show nonadditive expression than genes whose parental transcript levels were equal.The higher proportions of probe sets with expression level that differed from the parental midparent value and that were more extreme than either parental value in the heterotic hybrids compared to a non-heterotic hybrid were also found using RMA. We conclude that nonadditive expression of transcript levels may contribute to heterosis for biomass yield in alfalfa.Heterosis is a phenomenon in which offspring show increased fitness relative to their parents [1]. In classic quantitative genetics, three main hypotheses have been proposed to explain heterosis [2]. One is the dominance hypothesis, which suggests heterosis results from the complementation of favorable alleles of different loci in F1 hybrids. Under the dominance hypothesis, each heterozygous locus in F1 hybrids contributes to a trait
Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae
Brooke D Peterson-Burch, Dan Nettleton, Daniel F Voytas
Genome Biology , 2004, DOI: 10.1186/gb-2004-5-10-r78
Abstract: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution was distinctly non-uniform. Although both Pseudoviridae and Metaviridae tend to cluster within pericentromeric heterochromatin, this association is significantly more pronounced for all three Metaviridae sublineages (Metavirus, Tat and Athila). Among these, Tat and Athila are strictly associated with pericentromeric heterochromatin.The non-uniform genomic distribution of the Pseudoviridae and the Metaviridae can be explained by a variety of factors including target-site bias, selection against integration into euchromatin and pericentromeric accumulation of elements as a result of suppression of recombination. However, comparisons based on the age of elements and their chromosomal location indicate that integration-site specificity is likely to be the primary factor determining distribution of the Athila and Tat sublineages of the Metaviridae. We predict that, like retroelements in yeast, the Athila and Tat elements target integration to pericentromeric regions by recognizing a specific feature of pericentromeric heterochromatin.Endogenous retroviruses and long terminal repeat (LTR) retrotransposons (collectively called retroelements) generally comprise a significant portion of higher eukaryotic genomes. Dismissed as parasitic or 'junk' DNA, these sequences have traditionally received less attention than sequences contributing to the functional capacity of the organism. This perspective has changed with the completion of several eukaryotic genome sequences. The contributions of retroele
Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution
Lex Flagel, Joshua Udall, Dan Nettleton, Jonathan Wendel
BMC Biology , 2008, DOI: 10.1186/1741-7007-6-16
Abstract: We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 gene pairs. This comparison permitted partitioning of homoeolog expression biases into those arising from genomic merger and those resulting from polyploidy. Within allopolyploid Gossypium, approximately 24% of the genes with biased (unequal contributions from the two homoeologous copies) expression patterns are inferred to have arisen as a consequence of genomic merger, indicating that a substantial fraction of homoeolog expression biases occur instantaneously with hybridization. The remaining 76% of biased homoeologs reflect long-term evolutionary forces, such as duplicate gene neofunctionalization and subfunctionalization. Finally, we observed a greater number of genes biased toward the paternal D-genome and that expression biases have tended to increases during allopolyploid evolution.Our results indicate that allopolyploidization entails significant homoeolog expression modulation, both immediately as a consequence of genomic merger, and secondarily as a result of long-term evolutionary transformations in duplicate gene expression.A hallmark of angiosperm genome organization is gene redundancy. Redundant genome segments have been identified in the composition and architecture of modern-day angiosperm genomes suggesting one or more ancient genome duplication events [1-3]. This has led to considerable interest in the evolution of the resulting duplicated genes. A key issue has been the identification of factors that enhance the retention of duplicate gene pairs and their potential for adaptive diversification or subfunctionalization (the partitioning of ancestral function). Mechanisms such as the maintenance o
Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs
Yi Jia,Damon R. Lisch,Kazuhiro Ohtsu,Michael J. Scanlon,Dan Nettleton,Patrick S. Schnable
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000737
Abstract: Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, >6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant.
Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)
Sanzhen Liu, Cheng-Ting Yeh, Ho Man Tang, Dan Nettleton, Patrick S. Schnable
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036406
Abstract: Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples by analyzing the same RNA-Seq data using an empirical Bayesian approach. In addition, analysis of the RNA-Seq data provides information on the effects of the mutant on global patterns of gene expression at no extra cost. In combination these results greatly simplify gene cloning experiments. To demonstrate the utility of this strategy BSR-Seq was used to clone the glossy3 (gl3) gene of maize. Mutants of the glossy loci exhibit altered accumulation of epicuticular waxes on juvenile leaves. By subjecting the reference allele of gl3 to BSR-Seq, we were able to map the gl3 locus to an ~2 Mb interval. The single gene located in the ~2 Mb mapping interval whose expression was down-regulated in the mutant pool was subsequently demonstrated to be the gl3 gene via the analysis of multiple independent transposon induced mutant alleles. The gl3 gene encodes a putative myb transcription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.
Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin
Ceren Ciraci, Christopher K Tuggle, Michael J Wannemuehler, Dan Nettleton, Susan J Lamont
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-545
Abstract: The 38535-probeset Affymetrix GeneChip Chicken Genome array was used to profile transcriptional response to endotoxin 1, 2, 4, and 8 hours post stimulation (hps). Using a maximum FDR (False Discovery Rate) of 0.05 to declare genes as differentially expressed (DE), we found 13, 33, 1761 and 61 DE genes between endotoxin-stimulated versus non-stimulated cells at 1, 2, 4 and 8 hps, respectively. QPCR demonstrated that endotoxin exposure significantly affected the mRNA expression of IL1B, IL6, IL8, and TLR15, but not IL10 and IFNG in HD 11 cells. Ingenuity Pathway Analysis showed that 10% of the total DE genes were involved in inflammatory response. Three, 9.7, 96.8, and 11.8% of the total DE inflammatory response genes were significantly differentially expressed with endotoxin stimulation at 1, 2, 4 and 8 hps, respectively. The NFKBIA, IL1B, IL8 and CCL4 genes were consistently induced at all times after endotoxin treatment. NLRC5 (CARD domain containing, NOD-like receptor family, RCJMB04_18i2), an intracellular receptor, was induced in HD11 cells treated with endotoxin.As above using an in vitro model of chicken response to endotoxin, our data revealed the kinetics of gene networks involved in host response to endotoxin and extend the known complexity of networks in chicken immune response to Gram-negative bacteria such as Salmonella. The induction of NFKBIA, IL1B, IL8, CCL4 genes is a consistent signature of host response to endotoxin over time. We make the first report of induction of a NOD-like receptor family member in response to Salmonella endotoxin in chicken macrophages.Determining the effects of endotoxin from Salmonella typhimurium in chicken macrophages is an in vitro model to characterize the transcription profiles of one important cell type in the chickens' immune response. Endotoxin is a complex lipopolysaccharide (LPS) found in the outer cell membrane of Gram-negative bacteria that is responsible for membrane organization and stability [1] and differs f
Ten Tips for a Great Marriage according to Friedrich Nietzsche
S Nettleton
Indo-Pacific Journal of Phenomenology , 2009,
Abstract: Friendship is the highest form of love, according to the German philosopher Friedrich Nietzsche, because great friends inspire each other and can even push each other towards the ideal of the übermensch. While he was sceptical that many people would be strong enough for this kind of higher relationship, Nietzsche saw friendship as essential to a good marriage. Sex, in contrast, creates complications, because a relationship based on romantic feelings is unlikely to endure a lifetime. Furthermore, the ontological differences between men and women tend to turn love into a war. In order to overcome the power games in the arena of love, Nietzsche thus challenges lovers to be great friends. Drawing on Nietzsche’s plethora of aphorisms on friendship, marriage, sex and power relationships, this paper outlines how Nietzsche thought the institution of and approach to marriage could be reinvigorated in ways conducive to more successful relationships and greater human achievements. While some of Nietzsche’s ideas about marriage at first appear to be outrageous, much of what Nietzsche recommends is as relevant and challenging today as it was in his own time. Indeed, Nietzsche himself prophesied that the world would not be ready for his ideas until “sometime around the year 2000” (Fuss & Shapiro, 1971, p. 91).
Profile: Tessa Nettleton
Tessa Nettleton
Partnership : the Canadian Journal of Library and Information Practice and Research , 2010,
Abstract:
Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome
Sanzhen Liu,Cheng-Ting Yeh,Tieming Ji,Kai Ying,Haiyan Wu,Ho Man Tang,Yan Fu,Dan Nettleton,Patrick S. Schnable
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000733
Abstract: The Mu transposon system of maize is highly active, with each of the ~50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar ~215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ~965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of the Mu transposon system. The distribution of >40,000 non-redundant Mu insertion sites was strikingly non-uniform, such that rates increased in proportion to distance from the centromere. An identified putative Mu transposase binding consensus site does not explain this non-uniformity. An integrated genetic map containing more than 10,000 genetic markers was constructed and aligned to the sequence of the maize reference genome. Recombination rates (cM/Mb) are also strikingly non-uniform, with rates increasing in proportion to distance from the centromere. Mu insertion site frequencies are strongly correlated with recombination rates. Gene density does not fully explain the chromosomal distribution of Mu insertion and recombination sites, because pronounced preferences for the distal portion of chromosome are still observed even after accounting for gene density. The similarity of the distributions of Mu insertions and meiotic recombination sites suggests that common features, such as chromatin structure, are involved in site selection for both Mu insertion and meiotic recombination. The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.
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