Myth and History: A General Model and Its Application to the Bible

This paper focuses upon the prevalent complementary definitions of myth and history and questions their analytic utility with reference to literary documents that bespeak the transition between mythic and historic cognition. In the style of ethnosemantic analysis, these definitions are treated as a semantic domain and subjected to formal analysis. The components elicited constitute a new definition—more precisely, a two-dimensional model of the relationship between myth and history. Subsequently, the model is applied to a series of books from the Bible with the conclusion that men and women are structurally equal since, in their roles as social actors, both represent different components of myth as well as history.     

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.     

Neuronal Control of Mucus Secretion by Leeches: Toward a General Theory for Serotonin

The large Retzius cells are serotonin-containing neurons whoseimpulse activity controls the secretion of mucus from the skinof leeches. Serotonin elicits the secretion of mucus withoutany apparent synaptic transfers in either the central or peripheralnervous systems. Such a secretogogue function may be more generalas serotonin controls the secretion of mucus from the gastrointestinaltract of mammals and from the ciliated gills of bivalved molluscs.Furthermore, the qualitative and quantitative distribution ofserotonin in molluscs, annelids, arthropods, and vertebratescorresponds approximately with mucosecretory structures. Serotoninappears also to control other secretory functions in some ofthese animals. It is proposed therefore that serotonin mightoften function in controlling secretion.     

分形及其在植物研究中的应用

本文着重介绍了非线性科学热点之一的分形理论,并综述了分形理论在植物结构模拟、植物群落研究、景观格局研究、树木冠层特征研究、木材学研究、作物根系研究等方面的应用进展以及分维数求算方法研究进展,最后,对非线性理论在植物研究领域应用前景进行了展望。     

分形及其在植物研究中的应用

本文着重介绍了非线性科学热点之一的分形理论,并综述了分形理论在植物结构模拟、植物群落研究、景观格局研究、树木冠层特征研究、木材学研究、作物根系研究等方面的应用进展以及分维数求算方法研究进展,最后,对非线性理论在植物研究领域应用前景进行了展望。     

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.     

CorSig: A General Framework for Estimating Statistical Significance of Correlation and Its Application to Gene Co-Expression Analysis

With the rapid increase of omics data, correlation analysis has become an indispensable tool for inferring meaningful associations from a large number of observations. Pearson correlation coefficient (PCC) and its variants are widely used for such purposes. However, it remains challenging to test whether an observed association is reliable both statistically and biologically. We present here a new method, CorSig, for statistical inference of correlation significance. CorSig is based on a biology-informed null hypothesis, i.e., testing whether the true PCC (ρ) between two variables is statistically larger than a user-specified PCC cutoff (τ), as opposed to the simple null hypothesis of ρ = 0 in existing methods, i.e., testing whether an association can be declared without a threshold. CorSig incorporates Fisher''s Z transformation of the observed PCC (r), which facilitates use of standard techniques for p-value computation and multiple testing corrections. We compared CorSig against two methods: one uses a minimum PCC cutoff while the other (Zhu''s procedure) controls correlation strength and statistical significance in two discrete steps. CorSig consistently outperformed these methods in various simulation data scenarios by balancing between false positives and false negatives. When tested on real-world Populus microarray data, CorSig effectively identified co-expressed genes in the flavonoid pathway, and discriminated between closely related gene family members for their differential association with flavonoid and lignin pathways. The p-values obtained by CorSig can be used as a stand-alone parameter for stratification of co-expressed genes according to their correlation strength in lieu of an arbitrary cutoff. CorSig requires one single tunable parameter, and can be readily extended to other correlation measures. Thus, CorSig should be useful for a wide range of applications, particularly for network analysis of high-dimensional genomic data.

Software Availability

A web server for CorSig is provided at http://202.127.200.1:8080/probeWeb. R code for CorSig is freely available for non-commercial use at http://aspendb.uga.edu/downloads.     

A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum

While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.     

Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology

We present here a self-contained analytic review of the role of stochastic factors acting on a virus population. We develop a simple one-locus, two-allele model of a haploid population of constant size including the factors of random drift, purifying selection, and random mutation. We consider different virological experiments: accumulation and reversion of deleterious mutations, competition between mutant and wild-type viruses, gene fixation, mutation frequencies at the steady state, divergence of two populations split from one population, and genetic turnover within a single population. In the first part of the review, we present all principal results in qualitative terms and illustrate them with examples obtained by computer simulation. In the second part, we derive the results formally from a diffusion equation of the Wright-Fisher type and boundary conditions, all derived from the first principles for the virus population model. We show that the leading factors and observable behavior of evolution differ significantly in three broad intervals of population size, N. The “neutral limit” is reached when N is smaller than the inverse selection coefficient. When N is larger than the inverse mutation rate per base, selection dominates and evolution is “almost” deterministic. If the selection coefficient is much larger than the mutation rate, there exists a broad interval of population sizes, in which weakly diverse populations are almost neutral while highly diverse populations are controlled by selection pressure. We discuss in detail the application of our results to human immunodeficiency virus population in vivo, sampling effects, and limitations of the model.     

A Practical Approach to Evaluation of the Germicidal Efficiency of a General Purpose Military Disinfectant

The bactericidal activity of a general purpose disinfectant consisting of 25% sodium-o-phenylphenolate and 75% sodium-4- and 6-chloro-2-phenylphenolate was evaluated by a simulated in-use, surface-square dilution method. Common floor (asphalt, rubber, and unglazed tiles) and wall (stainless steel tile, ceramic tile, and painted wood) surfaces of various porosities and compositions were selected to simulate actual-use conditions.

The method used consisted of inoculating the surfaces of 1-in. square sections of floor and wall covering with a test organism, air-drying the inoculated surface, applying the disinfectant, allowing it to act for 10 min, and recovering the survivors by plating. Confirmatory results of the standard phenol coefficient and use-dilution tests indicated 700 ppm of the disinfectant to be a safe use concentration. The in-use surface-square dilution studies have shown that this is a more than adequate safe concentration for stainless steel, both glazed and unglazed ceramic tile, and nonwaxed surface of asphalt tile. However, concentrations ranging between 2,500 and 6,000 ppm for plastic-fortified rubber tile, 1,500 and 2,000 ppm for waxed asphalt tile, and 2,000 ppm for painted wood were required to achieve 99.9% reduction of either Salmonella choleraesuis or Salmonella schottmuelleri. These results indicate that a disinfectant concentration derived from the Association of Official Agricultural Chemists use-dilution test cannot always be relied upon to provide a dependable index to actual safe use-dilution when a disinfectant is supplied to certain wall or floor surfaces.