CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

Bidirectional selection for olfactory response to acetaldehyde and ethanol in Drosophila melanogaster

Drosophila melanogaster adults were successfully selected for increased and decreased olfactory response to different concentrations of acetaldehyde and ethanol, using a choice type olfactometer. The response to selection was not concentration specific. Lines were also tested with n-propanol, n-butanol, acetic acid, propionic acid, benzaldehyde, methyl acetate, ethyl acetate and 3-hydroxybutan-2-one. The behavior of the lines was similar for most of these chemicals, indicating an odorant specific response to selection. However, ethanol selected lines differed in their response to n-propanol and possibly n-butanol, suggesting a role for the alcohol group in determining the specificity of genetic variation in olfactory response. Utilization of acetic acid, ethanol and acetaldehyde as resources by the selected lines was tested using adult longevity. The only significant result was that lines selected for increased attraction to ethanol ulitised 9 p. 100 and 12 p. 100 ethanol more than lines selected for decreased attraction. Gene frequencies were monitored at 3 enzyme loci – alcohol dehydrogenase, triose phosphate isomerase, α-glycerophosphate dehydrogenase – associated with the metabolism of ethanol and acetaldehyde. There were no changes associated with the metabolism of ethanol and acetaldehyde. There were no changes associated with the response to selection, and the ADH-F allele increased in both selected and unselected lines

Genome-wide transcription analysis of clinal genetic variation in Drosophila.

Clinal variation in quantitative traits is widespread, but its genetic basis awaits identification. Drosophila melanogaster shows adaptive, clinal variation in traits such as body size along latitudinal gradients on multiple continents. To investigate genome wide transcription differentiation between North and South that might contribute to the clinal phenotypic variation, we compared RNA expression patterns during development of D. melanogaster from tropical northern and temperate southern populations using whole genome tiling arrays. We found that genes that were differentially expressed between the cline ends were generally associated with metabolism and growth, and experimental alteration of expression of a sample of them generally resulted in altered body size in the predicted direction, sometimes significantly so. We further identified the serpent (srp) transcription factor binding sites to be enriched near genes up-regulated in expression in the south. Analysis of clinal populations revealed a significant cline in the expression level of srp. Experimental over-expression of srp increased body size, as predicted from its clinal expression pattern, suggesting that it may be involved in regulating adaptive clinal variation in Drosophila. This study identified a handful of genes that contributed to clinal phenotypic variation through altered gene expression level, yet misexpression of individual gene led to modest body size change

Effects of beta-alanine supplementation on brain homocarnosine/carnosine signal and cognitive function: an exploratory study

Objectives: Two independent studies were conducted to examine the effects of 28 d of beta-alanine supplementation at 6.4 g d-1 on brain homocarnosine/carnosine signal in omnivores and vegetarians (Study 1) and on cognitive function before and after exercise in trained cyclists (Study 2). Methods: In Study 1, seven healthy vegetarians (3 women and 4 men) and seven age- and sex-matched omnivores undertook a brain 1H-MRS exam at baseline and after beta-alanine supplementation. In study 2, nineteen trained male cyclists completed four 20-Km cycling time trials (two pre supplementation and two post supplementation), with a battery of cognitive function tests (Stroop test, Sternberg paradigm, Rapid Visual Information Processing task) being performed before and after exercise on each occasion. Results: In Study 1, there were no within-group effects of beta-alanine supplementation on brain homocarnosine/carnosine signal in either vegetarians (p = 0.99) or omnivores (p = 0.27); nor was there any effect when data from both groups were pooled (p = 0.19). Similarly, there was no group by time interaction for brain homocarnosine/carnosine signal (p = 0.27). In study 2, exercise improved cognitive function across all tests (P0.05) of beta-alanine supplementation on response times or accuracy for the Stroop test, Sternberg paradigm or RVIP task at rest or after exercise. Conclusion: 28 d of beta-alanine supplementation at 6.4g d-1 appeared not to influence brain homocarnosine/ carnosine signal in either omnivores or vegetarians; nor did it influence cognitive function before or after exercise in trained cyclists

Analyses of density-dependent effects are needed to understand how and when Wolbachia can control dengue vectors

Releases of Wolbachia-infected mosquitoes have been shown to be an effective method of controlling Aedes aegypti, the main vector of dengue fever, in Australia. A study in BMC Biology from Penelope Hancock and others shows that incorporation of density-dependent effects into population models can provide major improvements in understanding how and when the infected populations can become established

The analysis of quantitative variation in natural populations with isofemale strains

Isofemale strains are having an increasing role in the analysis of variability of ecological and behavioural traits in natural populations. This paper therefore considers the association between heritability and phenotypic variation within and between isofemale strains. Heritability from an isofemale strain analysis approximates narrow heritability over a wide range of dominance values, particularly when genes contributing to variation in a trait are at intermediate frequencies. Meaningful heritability estimates require that isofemale strains are maintained at a population size greater than 50 and tested within 5 generations after establishment. Values of heritabilities for morphological traits in Drosophila melanogaster were similar to those estimated from a conventional sib analysis. Published data on isofemale strains can therefore be put into a theoretical framework. The contribution of isofemale strain analyses to the debate about the number of loci affection variation in quantitative traits is briefly discussed

The dangers of irreversibility in an age of increased uncertainty: revisiting plasticity in invertebrates

Plasticity in traits in response to environmental conditions can increase fitness, expanding the range of environments within which a genotype can generate viable and productive phenotypes, and therefore when and where populations can persist and diversify in ecological space. Adaptive forms of plasticity in invertebrates are diverse, ranging from polyphenism and diapause to behavioural thermoregulation and optimal foraging. Local patterns of environmental variation and developmental constraints will dictate which of these forms evolves. Here we review the core idea that the use of narrow developmental windows by invertebrates to attain specific types of phenotypic changes reduces their reversibility, while increasing their magnitude. These tradeoffs dictate the costs and effectiveness of plasticity in buffering environmental variation. In particular, plastic responses to narrow developmental or environmental windows increase fitness costs when predicted environmental challenges do not materialise, or when the environment changes in unpredictable ways. We then explore the converse idea that increasing trait reversibility depends on extending the period for which genotypes are sensitive to the environment, but also narrows the range of plastic phenotypes that can be generated. Considering these findings together, we would expect that the costs, benefits and constraints of reversible versus irreversible plasticity affect the rate and magnitude of adaptive responses to rapidly changing and novel environments. However, such predictions have rarely been tested or included in theoretical models. Identifying this knowledge gap leads us to propose new research directions to provide a deeper understanding of the evolution of plasticity in invertebrates and other organisms. We illustrate these possible directions through examples of Drosophila adapting to thermal stress