motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences

Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site motifs for a given transcription factor (TF) protein. Binding site motifs impart regulatory function by providing TFs the opportunity to bind to genomic elements and thereby affect the expression of nearby genes. Evolutionary changes to such functional DNA are hypothesized to be major contributors to phenotypic diversity within and between species; but despite the importance of TF motifs for gene expression, no method exists to test for motif loss or gain. Assuming that motif counts are Binomially distributed, and allowing for dependencies between motif instances in evolutionarily related sequences, we derive the probability mass function of the difference in motif counts between two nucleotide sequences. We provide a method to numerically estimate this distribution from genomic data and show through simulations that our estimator is accurate. Finally, we introduce the R package {\tt motifDiverge} that implements our methodology and illustrate its application to gene regulatory enhancers identified by a mouse developmental time course experiment. While this study was motivated by analysis of regulatory motifs, our results can be applied to any problem involving two correlated Bernoulli trials

Shared Governance in an Adult Education Doctoral Program: “Self-Directed Learning meets Democratic Process” – A Delicate Balance of Intent, Implementation, and Impact

This symposium explores the governance component offered within a doctoral program in which students were given the opportunity to engage in collective decision-making through democratic process. Panelists, most of whom were research participants for the dissertation upon which this exploration is based, represent cohort groups from 1996 through 2007

Impact of Hemlock Woolly Adelgid (Hemiptera: Adelgidae) Infestation on the Jasmonic Acid-Elicited Defenses of Tsuga canadensis (Pinales: Pinaceae)

Hemlock woolly adelgid is an invasive piercing-sucking insect in eastern North America, which upon infestation of its main host, eastern hemlock (‘hemlock’), improves attraction and performance of folivorous insects on hemlock. This increased performance may be mediated by hemlock woolly adelgid feeding causing antagonism between the the jasmonic acid and other hormone pathways. In a common garden experiments using hemlock woolly adelgid infestation and induction with methyl jasmonate (MeJA) and measures of secondary metabolite contents and defense-associated enzyme activities, we explored the impact of hemlock woolly adelgid feeding on the local and systemic induction of jasmonic acid (JA)-elicited defenses. We found that in local tissue hemlock woolly adelgid or MeJA exposure resulted in unique induced phenotypes, whereas the combined treatment resulted in an induced phenotype that was a mixture of the two individual treatments. We also found that if the plant was infested with hemlock woolly adelgid, the systemic response of the plant was dominated by hemlock woolly adelgid, regardless of whether MeJA was applied. Interestingly, in the absence of hemlock woolly adelgid, hemlock plants had a very weak systemic response to MeJA. We conclude that hemlock woolly adelgid infestation prevents systemic induction of JA-elicited defenses. Taken together, compromised local JA-elicited defenses combined with weak systemic induction could be major contributors to increased folivore performance on hemlock woolly adelgid-infested hemlock

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

Natural-abundance radiocarbon as a tracer of assimilation of petroleum carbon by bacteria in salt marsh sediments

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 70 (2006): 1761-1771, doi:10.1016/j.gca.2005.12.020.The natural abundance of radiocarbon (14C) provides unique insight into the source and cycling of sedimentary organic matter. Radiocarbon analysis of bacterial phospholipid lipid fatty acids (PLFAs) in salt-marsh sediments of southeast Georgia (USA) – one heavily contaminated by petroleum residues – was used to assess the fate of petroleum-derived carbon in sediments and incorporation of fossil carbon into microbial biomass. PLFAs that are common components of eubacterial cell membranes (e.g., branched C15 and C17, 10-methyl-C16) were depleted in 14C in the contaminated sediment (mean Δ14C value of +25 ± 19 ‰ for bacterial PLFAs) relative to PLFAs in uncontaminated “control” sediment (Δ14C = +101 ± 12‰). We suggest that the 14C-depletion in bacterial PLFAs at the contaminated site results from microbial metabolism of petroleum and subsequent incorporation of petroleum-derived carbon into bacterial membrane lipids. A mass balance calculation indicates that 6-10% of the carbon in bacterial PLFAs at the oiled site could derive from petroleum residues. These results demonstrate that even weathered petroleum may contain components of sufficient lability to be a carbon source for biomass production by marsh sediment microorganisms. Furthermore, a small but significant fraction of fossil carbon is assimilated even in the presence of a much larger pool of presumably more-labile and faster-cycling carbon substrates.This study was supported by Georgia Sea Grant (RR100-221/926784), the National Science Foundation (OCE-9911678) and NOSAMS (thanks to J. M. Hayes)

On Linear Algebraic Representation of Time-span and Prolongational Trees

In constructive music theory, such as Schenkerian analysis and the Generative Theory of Tonal Music (GTTM), the hierarchical importance of pitch events is conveniently represented by a tree structure. Although a tree is easy to recognize and has high visibility, such an intuitive representation can hardly be treated in mathematical formalization. Especially in GTTM, the conjunction height of two branches is often arbitrary, contrary to the notion of hierarchy. Since a tree is a kind of graph, and a graph is often represented by a matrix, we show the linear algebraic representation of trees, specifying conjunction heights. Thereafter, we explain the ‘reachability’ between pitch events (corresponding to information about reduction) by the multiplication of matrices. In addition we discuss multiplication with vectors representing a sequence of harmonic functions, and suggest the notion of stability. Finally, we discuss operations between matrices to model compositional processes with simple algebraic operations

Rhizosphere engineering: Innovative improvement of root environment

© 2017 Elsevier B.V.The ability of roots to extract water and nutrients from soil depends on the biophysical properties of the rhizosphere, which are strongly influenced by mucilage secretion. The aim of this study was to introduce the concept of rhizoligands to engineer the biophysical properties of the rhizosphere. A rhizoligand is defined as an additive that increases the wettability of the rhizosphere and links the mucilage network to main intimate contact with the root surface. We hypothesize that rhizoligands: i) facilitate the rewetting of the rhizosphere during repeated drying and wetting cycles; ii) enhance rhizosheath formation; iii) increase enzyme activities in the rhizosphere; and iv) increase plant biomass. A commercial surfactant was selected as the prototype rhizoligand to test the effect on the rhizosphere biophysical properties of white lupin grown in quartz sand and subjected to six drying-rewetting cycles. Half of the plants were irrigated with water and the other half with the rhizoligand solution. When plants were 50 days old, we measured: i) soil water content; ii) rhizosheath mass; iii) activity of selected enzymes; iv) carbon content in the rhizosphere; and v) plant biomass. Rhizoligand increased rewetting rate of the rhizosphere after drying and subsequent rewetting, resulting in a greater soil water content. Rhizosheath formation was improved in plants irrigated with rhizoligand and sand particles attached to the roots increased by 1.64 times compared to plants irrigated with water. Activity of the enzymes chitinase, sulfatase, and β-glucosidase were 4, 7.9, and 1.5 times greater in the rhizosphere of plants irrigated with rhizoligand than in the rhizosphere of plants irrigated with water. Plant biomass was 1.2 fold greater in samples irrigated with rhizoligand solution than in samples irrigated with water. We conclude that application of rhizoligand improves plant performance by influencing the water dynamics in the rhizosphere and the plant, increasing the mechanical stability of the rhizosheaths and increasing the enzyme activities in the rhizosphere. Such effects are probably triggered by the interaction between mucilage and the applied rhizoligand, which reduces mucilage swelling (possibly by cross-linking mucilage polymers) and thus by increasing its viscosity keeps the mucilage close to the root surface. We propose the rhizoligand concept as a strategy to engineer the rhizosphere properties and to improve plant tolerance to water shortage

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

GC-biased gene conversion (gBGC) is a recombination-associated evolutionary process that accelerates the fixation of guanine or cytosine alleles, regardless of their effects on fitness. gBGC can increase the overall rate of substitutions, a hallmark of positive selection. Many fast-evolving genes and noncoding sequences in the human genome have GC-biased substitution patterns, suggesting that gBGC—in contrast to adaptive processes—may have driven the human changes in these sequences. To investigate this hypothesis, we developed a substitution model for DNA sequence evolution that quantifies the nonlinear interacting effects of selection and gBGC on substitution rates and patterns. Based on this model, we used a series of lineage-specific likelihood ratio tests to evaluate sequence alignments for evidence of changes in mode of selection, action of gBGC, or both. With a false positive rate of less than 5% for individual tests, we found that the majority (76%) of previously identified human accelerated regions are best explained without gBGC, whereas a substantial minority (19%) are best explained by the action of gBGC alone. Further, more than half (55%) have substitution rates that significantly exceed local estimates of the neutral rate, suggesting that these regions may have been shaped by positive selection rather than by relaxation of constraint. By distinguishing the effects of gBGC, relaxation of constraint, and positive selection we provide an integrated analysis of the evolutionary forces that shaped the fastest evolving regions of the human genome, which facilitates the design of targeted functional studies of adaptation in humans