Evolution of genetic variability and the advantage of sex and recombination in changing environments

The role of recombination and sexual reproduction in enhancing adaptation and population persistence in temporally varying environments is investigated on the basis of a quantitative-genetic multilocus model. Populations are finite, subject to density-dependent regulation with a finite growth rate, diploid, and either asexual or randomly mating and sexual with or without recombination. A quantitative trait is determined by a finite number of loci at which mutation generates genetic variability. The trait is under stabilizing selection with an optimum that either changes at a constant rate in one direction, exhibits periodic cycling, or fluctuates randomly. It is shown by Monte Carlo simulations that if the directional-selection component prevails, then freely recombining populations gain a substantial evolutionary advantage over nonrecombining and asexual populations that goes far beyond that recognized in previous studies. The reason is that in such populations, the genetic variance can increase substantially and thus enhance the rate of adaptation. In nonrecombining and asexual populations, no or much less increase of variance occurs. It is explored by simulation and mathematical analysis when, why, and by how much genetic variance increases in response to environmental change. In particular, it is elucidated how this change in genetic variance depends on the reproductive system, the population size, and the selective regime, and what the consequences for population persistence are

Additive Genetic Variation under Intraspecific Competition and Stabilizing Selection: A Two-Locus Study [Revised June 2002]

A diallelic two-locus model is investigated in which the loci determine the genotypic value of a quantitative trait additively. Fitness has two components: stabilizing selection on the trait and a frequency-dependent component, as induced for instance if the ability to utilize different food resource depend on this trait. Since intraspecific competition induces disruptive selection, this model leads to a conflict of selective forces. We study how the underlying genetics (recombination rate and allelic effects) interacts with the selective forces, and explore the resulting equilibrium structure. For the special case of equal effects, global stability results are proved. Unless the locus effects are sufficiently different, the genetic variance maintained at equilibrium displays a threshold-like dependence on the strength of competition. For loci with equal effects, the equilibrium fitnesses of genotypic value exhibit disruptive selection if and only if competition is strong enough to maintain a stable two-locus polymorphism. For unequal effects, disruptive selection can be observed for weaker competition and in the absence of a stable polymorphism

Former students discuss middle school science journalism : a qualitative study of personally meaningful disciplinary writing.

This qualitative research study explores the experiences of six middle school students with science news writing (SciJourn) after they have transitioned to high school. The qualitative method of case study was used with the data analyzed through the method of constructivist grounded theory. SciJourn is a disciplinary approach to science literacy that allows students to choose and research their own topic, interact with experts in the field, construct their own knowledge, and have the opportunity to publish in an on-line science newspaper (Scijourner.org). Theoretically, this research draws on science as social practice where literacy learning is cognitively complex, is situated in the social character of human understanding, and involves social co-participation situated in a learning community. With the renewed focus on science literacy and an emphasis on Writing in the Disciplines (WID), research has shown that a shift from general to disciplinary literacy strategies has significantly increased students’ skill and achievement with both higher and lower achieving students. v The six case study students who participated in SciJourn in middle school wrote reflective letters, were interviewed twice, and three participated in a group interview/group activity. Data analysis using the constant comparative method of grounded theory revealed the themes of Learning Language (increased knowledge of writing process and structure), Learning through Language (interest in science content and knowledge of science practice), and Living Language (students found meaning in their experience). Analysis showed the significance of including authentic disciplinary literacy assignments in all content area classrooms. The following appear to be the essential elements that increase the meaning and value of the SciJourn experience for the students: Choosing own topic, having a connection, having a partner, interacting with the outside world (family, editor, experts, audience), and the opportunity to publish. In addition, the key understanding of Negotiation with self and others (peers, family, the editor, experts, and/or an audience) revealed an emotional experience that contributed to increased engagement in the writing process and supported the development of confidence in their ability to complete an authentic writing assignment to a publishable piece

Genetic variation maintained in multilocus models of additive quantitative traits under stabilizing selection

Stabilizing selection for an intermediate optimum is generally considered to deplete genetic variation in quantitative traits. However, conflicting results from various types of models have been obtained. While classical analyses assuming a large number of independent additive loci with individually small effects indicated that no genetic variation is preserved under stabilizing selection, several analyses of two-locus models showed the contrary. We perform a complete analysis of a generalization of Wright's two-locus quadratic-optimum model and investigate numerically the ability of quadratic stabilizing selection to maintain genetic variation in additive quantitative traits controlled by up to five loci. A statistical approach is employed by choosing randomly 4000 parameter sets (allelic effects, recombination rates, and strength of selection) for a given number of loci. For each parameter set we iterate the recursion equations that describe the dynamics of gamete frequencies starting from 20 randomly chosen initial conditions until an equilibrium is reached, record the quantities of interest, and calculate their corresponding mean values. As the number of loci increases from two to five, the fraction of the genome expected to be polymorphic declines surprisingly rapidly, and the loci that are polymorphic increasingly are those with small effects on the trait. As a result, the genetic variance expected to be maintained under stabilizing selection decreases very rapidly with increased number of loci. The equilibrium structure expected under stabilizing selection on an additive trait differs markedly from that expected under selection with no constraints on genotypic fitness values. The expected genetic variance, the expected polymorphic fraction of the genome, as well as other quantities of interest, are only weakly dependent on the selection intensity and the level of recombination

Fluctuating Environments and the Role of Mutation in Maintaining Quantitative Genetic Variation

We study a class of genetic models in which a quantitative trait determined by several loci is subject to temporally fluctuating selection. Selection on the trait is assumed to be stabilizing, but with an optimum that varies periodically and may be perturbed stochastically. The population mates at random, is infinitely large, and has discrete generations. We pursue a statistical and numerical approach, covering a wide range of ecological and genetic parameters, to determine the potential of fluctuating environments in maintaining quantitative-genetic variation. Whereas, in contrast to some recent claims, this potential seems to be rather limited in the absence of recurrent mutation, in combination with it fluctuating environments may frequently generate high levels of additive genetic variation. It is investigated how the genetic variation maintained depends on the ecological parameters and on the underlying genetics

Remote soil moisture measurements

The degree of polarization of visible sunlight reflected from bare soils in agricultural test areas in the southwestern United States was measured by an airborne photopolarimeter. Surface soil specimens provided data concerning the surface moisture of the soil to which the polarization data were compared. The results indicate the feasibility of measuring soil surface moisture by airborne polarimeter instrumentation

A unified evaluation of iterative projection algorithms for phase retrieval

Iterative projection algorithms are successfully being used as a substitute of lenses to recombine, numerically rather than optically, light scattered by illuminated objects. Images obtained computationally allow aberration-free diffraction-limited imaging and the possibility of using radiation for which no lenses exist. The challenge of this imaging technique is transfered from the lenses to the algorithms. We evaluate these new computational ``instruments'' developed for the phase retrieval problem, and discuss acceleration strategies.Comment: 12 pages, 9 figures, revte

Nuclear DDX3 expression predicts poor outcome in colorectal and breast cancer

Purpose: DEAD box protein 3 (DDX3) is an RNA helicase with oncogenic properties that shuttles between the cytoplasm and nucleus. The majority of DDX3 is found in the cytoplasm, but a subset of tumors has distinct nuclear DDX3 localization of yet unknown biological significance. This study aimed to evaluate the significance of and mechanisms behind nuclear DDX3 expression in colorectal and breast cancer. Methods: Expression of nuclear DDX3 and the nuclear exporter chromosome region maintenance 1 (CRM1) was evaluated by immunohistochemistry in 304 colorectal and 292 breast cancer patient samples. Correlations between the subcellular localization of DDX3 and CRM1 and the difference in overall survival between patients with and without nuclear DDX3 were studied. In addition, DDX3 mutants were created for in vitro evaluation of the mechanism behind nuclear retention of DDX3. Results: DDX3 was present in the nucleus of 35% of colorectal and 48% of breast cancer patient samples and was particularly strong in the nucleolus. Nuclear DDX3 correlated with worse overall survival in both colorectal (hazard ratio [HR] 2.34, P<0.001) and breast cancer (HR 2.39, P=0.004) patients. Colorectal cancers with nuclear DDX3 expression more often had cytoplasmic expression of the nuclear exporter CRM1 (relative risk 1.67, P=0.04). In vitro analysis of DDX3 deletion mutants demonstrated that CRM1-mediated export was most dependent on the N-terminal nuclear export signal. Conclusion: Overall, we conclude that nuclear DDX3 is partially CRM1-mediated and predicts worse survival in colorectal and breast cancer patients, putting it forward as a target for therapeutic intervention with DDX3 inhibitors under development in these cancer types

Ag on Ge(111): 2D X-ray structure analysis of the (Wurzel)3 x (Wurzel)3 superstructure

We have studied the Ag/Ge(111)(Wurzel)3 x (Wurzel)3 superstructure by grazing-incidence X-ray diffraction. In our structural analysis we find striking similarities to the geometry of Au on Si(111). The Ag atoms form trimer clusters with an Ag-Ag distance of 2.94+-0.04°A with the centers of the trimers being located at the origins of the (Wurzel)3 x (Wurzel)3 lattice. The Ag layer is incomplete and at least one substrate layer is distorted

From cholera to corals: viruses as drivers of virulence in a major coral bacterial pathogen

Disease is an increasing threat to reef-building corals. One of the few identified pathogens of coral disease is the bacterium Vibrio coralliilyticus. In Vibrio cholerae, infection by a bacterial virus (bacteriophage) results in the conversion of non-pathogenic strains to pathogenic strains and this can lead to cholera pandemics. Pathogenicity islands encoded in the V. cholerae genome play an important role in pathogenesis. Here we analyse five whole genome sequences of V. coralliilyticus to examine whether virulence is similarly driven by horizontally acquired elements. We demonstrate that bacteriophage genomes encoding toxin genes with homology to those found in pathogenic V. cholerae are integrated in V. coralliilyticus genomes. Virulence factors located on chromosomal pathogenicity islands also exist in some strains of V. coralliilyticus. The presence of these genetic signatures indicates virulence in V. coralliilyticus is driven by prophages and other horizontally acquired elements. Screening for pathogens of coral disease should target conserved regions in these elements