One for All and All for One: Cross-Talk of Multiple Signals Controlling the Plant Phenotype

The plant hormone ethylene plays a pivotal role in steering various processes by regulating the biosynthesis, distribution, or signal transduction of other hormones. Ethylene also mediates the effects of other hormones. Similarly, hormones control the ethylene synthesis and signalling pathway. Eventually, integration of this network of signals leads to an appropriate morphological or biochemical response. Consequently, this cross-talk results in the characteristic plasticity associated with plant development. Here, the interplay of ethylene with other hormones is described for germination and seedling growth, stomatal control, and tissue elongation. The mechanisms by which this occurs are discussed in more detail.     

Properties of Statistical Tests of Neutrality for DNA Polymorphism Data

A class of statistical tests based on molecular polymorphism data is studied to determine size and power properties. The class includes TAJIMA''s D statistic as well as the D* and F* tests proposed by FU and LI. A new method of constructing critical values for these tests is described. Simulations indicate that TAJIMA''s test is generally most powerful against the alternative hypotheses of selective sweep, population bottleneck, and population subdivision, among tests within this class. However, even TAJIMA''s test can detect a selective sweep or bottleneck only if it has occurred within a specific interval of time in the recent past or population subdivision only when it has persisted for a very long time. For greatest power against the particular alternatives studied here, it is better to sequence more alleles than more sites.     

New Statistical Tests of Neutrality for DNA Samples from a Population

The purpose of this paper is to develop statistical tests of the neutral model of evolution against a class of alternative models with the common characteristic of having an excess of mutations that occurred a long time ago or a reduction of recent mutations compared to the neutral model. This class of population genetics models include models for structured populations, models with decreasing effective population size and models of selection and mutation balance. Four statistical tests were proposed in this paper for DNA samples from a population. Two of these tests, one new and another a modification of an existing test, are based on EWENS'' sampling formula, and the other two new tests make use of the frequencies of mutations of various classes. Using simulated samples and regression analyses, the critical values of these tests can be computed from regression equations. This approach for computing the critical values of a test was found to be appropriate and quite effective. We examined the powers of these four tests using simulated samples from structured populations, populations with linearly decreasing sizes and models of selection and mutation balance and found that they are more powerful than existing statistical tests of the neutral model of evolution.     

Statistical Properties of New Neutrality Tests Against Population Growth

Sebastian E. Ramos-Onsins and     

One for All or All for One: Heterogeneous Expression and Host Cell Lysis Are Key to Gene Transfer Agent Activity in Rhodobacter capsulatus

The gene transfer agent (RcGTA) of Rhodobacter capsulatus is the model for a family of novel bacteriophage-related genetic elements that carry out lateral transfer of essentially random host DNA. Genuine and putative gene transfer agents have been discovered in diverse genera and are becoming recognized as potentially an important source of genetic exchange and microbial evolution in the oceans. Despite being discovered over 30 years ago, little is known about many essential aspects of RcGTA biology. Here, we validate the use of direct fluorescence reporter constructs, which express the red fluorescent protein mCherry in R. capsulatus. A construct containing the RcGTA promoter fused to mCherry was used to examine the single-cell expression profiles of wild type and RcGTA overproducer R. capsulatus populations, under different growth conditions and growth phases. The majority of RcGTA production clearly arises from a small, distinct sub-set of the population in the wild type strain and a larger sub-set in the overproducer. The most likely RcGTA release mechanism concomitant with this expression pattern is host cell lysis and we present direct evidence for the release of an intracellular enzyme accompanying RcGTA release. RcGTA ORF s is annotated as a 'cell wall peptidase' but we rule out a role in host lysis and propose an alternative function as a key contributor to RcGTA invasion of a target cell during infection.     

Gene Frequency Distributions as a Test of Selective Neutrality

The analysis of differences between loci in the variance of gene frequency over populations within a species has been suggested as a method of detecting natural selection. It is shown that, in the absence of selection, the expected variation over loci depends strongly on the pattern of relationships between populations. The effect of structure within a species is always to increase the variation and therefore to reduce the power of the method.     

FtsZ in Bacterial Cytokinesis: Cytoskeleton and Force Generator All in One

Summary: FtsZ, a bacterial homolog of tubulin, is well established as forming the cytoskeletal framework for the cytokinetic ring. Recent work has shown that purified FtsZ, in the absence of any other division proteins, can assemble Z rings when incorporated inside tubular liposomes. Moreover, these artificial Z rings can generate a constriction force, demonstrating that FtsZ is its own force generator. Here we review light microscope observations of how Z rings assemble in bacteria. Assembly begins with long-pitch helices that condense into the Z ring. Once formed, the Z ring can transition to short-pitch helices that are suggestive of its structure. FtsZ assembles in vitro into short protofilaments that are ∼30 subunits long. We present models for how these protofilaments might be further assembled into the Z ring. We discuss recent experiments on assembly dynamics of FtsZ in vitro, with particular attention to how two regulatory proteins, SulA and MinC, inhibit assembly. Recent efforts to develop antibacterial drugs that target FtsZ are reviewed. Finally, we discuss evidence of how FtsZ generates a constriction force: by protofilament bending into a curved conformation.     

Experiments with the Site Frequency Spectrum

Evaluating the likelihood function of parameters in highly-structured population genetic models from extant deoxyribonucleic acid (DNA) sequences is computationally prohibitive. In such cases, one may approximately infer the parameters from summary statistics of the data such as the site-frequency-spectrum (SFS) or its linear combinations. Such methods are known as approximate likelihood or Bayesian computations. Using a controlled lumped Markov chain and computational commutative algebraic methods, we compute the exact likelihood of the SFS and many classical linear combinations of it at a non-recombining locus that is neutrally evolving under the infinitely-many-sites mutation model. Using a partially ordered graph of coalescent experiments around the SFS, we provide a decision-theoretic framework for approximate sufficiency. We also extend a family of classical hypothesis tests of standard neutrality at a non-recombining locus based on the SFS to a more powerful version that conditions on the topological information provided by the SFS.     

Visual Data Mining of Biological Networks: One Size Does Not Fit All

High-throughput technologies produce massive amounts of data. However, individual methods yield data specific to the technique used and biological setup. The integration of such diverse data is necessary for the qualitative analysis of information relevant to hypotheses or discoveries. It is often useful to integrate these datasets using pathways and protein interaction networks to get a broader view of the experiment. The resulting network needs to be able to focus on either the large-scale picture or on the more detailed small-scale subsets, depending on the research question and goals. In this tutorial, we illustrate a workflow useful to integrate, analyze, and visualize data from different sources, and highlight important features of tools to support such analyses.     

Learning Natural Selection from the Site Frequency Spectrum

Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality. We build upon recent work that connects many of these tests under a common framework, by describing how selective sweeps affect the scaled SFS. We show that the specific skew depends on many attributes of the sweep, including the selection coefficient and the time under selection. Using supervised learning on extensive simulated data, we characterize the features of the scaled SFS that best separate different types of selective sweeps from neutrality. We develop a test, SFselect, that consistently outperforms many existing tests over a wide range of selective sweeps. We apply SFselect to polymorphism data from a laboratory evolution experiment of Drosophila melanogaster adapted to hypoxia and identify loci that strengthen the role of the Notch pathway in hypoxia tolerance, but were missed by previous approaches. We further apply our test to human data and identify regions that are in agreement with earlier studies, as well as many novel regions.     

The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep

In the area of evolutionary theory, a key question is which portions of the genome of a species are targets of natural selection. Genetic hitchhiking is a theoretical concept that has helped to identify various such targets in natural populations. In the presence of recombination, a severe reduction in sequence diversity is expected around a strongly beneficial allele. The site frequency spectrum is an important tool in genome scans for selection and is composed of the numbers , where is the number of single nucleotide polymorphisms (SNPs) present in from individuals. Previous work has shown that both the number of low- and high-frequency variants are elevated relative to neutral evolution when a strongly beneficial allele fixes. Here, we follow a recent investigation of genetic hitchhiking using a marked Yule process to obtain an analytical prediction of the site frequency spectrum in a panmictic population at the time of fixation of a highly beneficial mutation. We combine standard results from the neutral case with the effects of a selective sweep. As simulations show, the resulting formula produces predictions that are more accurate than previous approaches for the whole frequency spectrum. In particular, the formula correctly predicts the elevation of low- and high-frequency variants and is significantly more accurate than previously derived formulas for intermediate frequency variants.     

Frequency Spectrum Method-Based Stress Analysis for Oil Pipelines in Earthquake Disaster Areas

When a long distance oil pipeline crosses an earthquake disaster area, inertial force and strong ground motion can cause the pipeline stress to exceed the failure limit, resulting in bending and deformation failure. To date, researchers have performed limited safety analyses of oil pipelines in earthquake disaster areas that include stress analysis. Therefore, using the spectrum method and theory of one-dimensional beam units, CAESAR II is used to perform a dynamic earthquake analysis for an oil pipeline in the XX earthquake disaster area. This software is used to determine if the displacement and stress of the pipeline meet the standards when subjected to a strong earthquake. After performing the numerical analysis, the primary seismic action axial, longitudinal and horizontal displacement directions and the critical section of the pipeline can be located. Feasible project enhancement suggestions based on the analysis results are proposed. The designer is able to utilize this stress analysis method to perform an ultimate design for an oil pipeline in earthquake disaster areas; therefore, improving the safe operation of the pipeline.     

Normal Approximations of Exact Tests in Configural Frequency Analysis

The most common tests for types and antitypes in configural frequency analysis are normal approximations of exact tests. In the paper such statistics under the complete independence model and under the fixed margins model are discussed. It turns out that these test statistics are not acceptable when the number of simultaneously performed tests is large or when the expected frequencies are small. In these cases, the use of exact tests is advocated and some existing computer programs for such tests are indicated. A normal approximation based on the strong version of the De Moivre-Laplace limit theorem is also discussed. Empirical examples are given from longitudinal data describing psychological development of boys.     

Frequency Spectrum of Transepithelial Potential Difference Reveals Transport-Related Oscillations

How epithelia transport fluid is a fundamental issue that is unresolved. Explanations offered include molecular engines, local transcellular osmosis, local paracellular osmosis, and paracellular fluid transport. On the basis of experimental and theoretical work done on corneal endothelium, a fluid transporting epithelium, we suggest electroosmotic coupling at the level of the intercellular junctions driven by the transendothelial electrical potential difference as an explanation of paracellular fluid transport. We collect frequency spectra of that potential difference in real-time. For what we believe is the first time for any epithelium, we report that, unexpectedly, the potential difference displays oscillations at many characteristic frequencies. We also show that on both stimulating cell activity and inhibiting ion transport mechanisms, there are corresponding changes in the oscillations amplitudes that mirror changes known previously in rates of fluid transport. We believe these findings provide a novel tool to study the kinetics of electrogenic elements such as channels and transporters, which from this evidence would give rise to current oscillations with characteristic periods going from 150 ms to 8 s.