The loss in hydrophobic surface area resulting from a Leu to Val mutation at the N-terminus of the aldehyde dehydrogenase presequence prevents import of the protein into mitochondria

An apparent conservative mutation, Leu to Val, at the second residue of the rat liver mitochondrial aldehyde dehydrogenase (ALDH) presequence resulted in a precursor protein that was not imported into mitochondria. Additional mutants were made to substitute various amino acids with nonpolar side chains for Leu2. The Ile, Phe, and Trp mutants were imported to an extent similar to that of the native precursor, but the Ala mutant was imported only about one-fourth as well. It was shown that the N-terminal methionine was removed from the L2V mutant in a reaction catalyzed by methionine aminopeptidase. The N-terminal methionine of native pALDH and the other mutant presequences was blocked, presumably by acetylation. Because of the difference in co-translational modification, the L2V mutant sustained a significant loss in the available hydrophobic surface of the presequence. Import competence was restored to the L2V mutant when it was translated using a system that did not remove Met1. The removal of an Arg-Gly-Pro helix linker segment (residues 11-14) from the L2V mutant, which shifted three leucine residues toward the N-terminus, also restored import competence. These results lead to the conclusion that a minimum amount of hydrophobic surface area near the N-termini of mitochondrial presequences is an essential property to determine their ability to be imported. As a result, both electrostatic and hydrophobic components must be considered when trying to understand the interactions between precursor proteins and proteins of the mitochondrial import apparatus.     

Fish, Flows and Flood Plains: Links between Freshwater Fishes and their Environment in the Murray-Darling River System, Australia

Knowledge of the biology of native fishes of the Murray-Darling Basin is based largely on studies conducted under hatchery conditions and on a limited number of recreationally important species. From observations that increases in water level in aquaculture ponds initiate spawning in some species, and from limited studies of wild fishes and studies in overseas floodplain river systems, a perception has emerged of the importance of flooding and the flood plain in the life cycles of Murray-Darling fishes in general. However, there is little confirmatory evidence of the use of temporary floodplain habitats by larvae, juveniles or adults. The significance of in-channel habitats, especially for rearing, has received little attention. Murray-Darling fish species can be placed into three life history modes, based mainly on spawning style and time and developmental intervals of larvae at first feeding. Fish in each group may be able to take advantage of floods if the timing is right and prey are plentiful, however, the larvae of some species are able to recruit under non-flood conditions within the main river channel. This forms the basis of the low flow recruitment hypothesis, which attempts to explain why some species spawn during the warmest months and lowest flows and how they are able to recruit under these conditions. This hypothesis is then placed in the context of the current state of knowledge of the relationships between flow and the biology of Murray-Darling fishes, specifically cues for spawning, movement and recruitment. The lack of widespread evidence for floodplain use by any life history interval of fish may be due to a paucity of study, however, there are some fundamental factors, such as the predictability of timing and duration of high flow events as well as the lack of coincidence of high flows and high temperatures in some regions of the Basin, which may be important in determining the use of floodplain habitats by fish.     

Model-free Analysis of Protein Dynamics: Assessment of Accuracy and Model Selection Protocols Based on Molecular Dynamics Simulation

The popular model-free approach to analyze NMR relaxation measurements has been examined using artificial amide (15)N relaxation data sets generated from a 10 nanosecond molecular dynamics trajectory of a dihydrofolate reductase ternary complex in explicit water. With access to a detailed picture of the underlying internal motions, the efficacy of model-free analysis and impact of model selection protocols on the interpretation of NMR data can be studied. In the limit of uncorrelated global tumbling and internal motions, fitting the relaxation data to the model-free models can recover a significant amount of quantitative information on the internal dynamics. Despite a slight overestimation, the generalized order parameter is quite accurately determined. However, the model-free analysis appears to be insensitive to the presence of nanosecond time scale motions with relatively small magnitude. For such cases, the effective correlation time can be significantly underestimated. As a result, proteins appear to be more rigid than they really are. The model selection protocols have a major impact on the information one can reliably obtain. The commonly employed protocol based on step-up hypothesis testing has severe drawbacks of oversimplification and underfitting. The consequences are that the order parameter is more severely overestimated and the correlation time more severely underestimated. Instead, model selection based on Bayesian Information Criteria (BIC), recently introduced to the model-free analysis by d'Auvergne and Gooley (2003), provides a better balance between bias and variance. More appropriate models can be selected, leading to improved estimate of both the order parameter and correlation time. In addition, the computational cost is significantly reduced and subjective parameters such as the significance level are unnecessary.     

A new hypothesis for species coexistence: male–male repulsion promotes coexistence of competing species

We propose a new hypothesis for species coexistence by considering behavioral interactions between individuals. The hypothesis states that repulsive behavior between conspecific males (male–male repulsion) creates space for competing species, which promotes their coexistence. This hypothesis can explain the coexistence of two competing species even when their ecological niches completely overlap in spatially homogeneous environments. In addition, the mechanisms underlying such behavior might play a role in enabling the coexistence of two species immediately after speciation, with little or no niche differentiation, as in the case of cichlid fish communities, for example. Although there is limited evidence supporting this hypothesis, it can nevertheless explain the occurrence of species coexistence and biodiversity, which cannot be explained by previous theories.     

Variable selection in Platanthera bifolia (Orchidaceae): phenotypic selection differed between sex functions in a drought year

We estimated selection on three morphological characters in the hermaphroditic, hawkmoth-pollinated orchid Platanthera bifolia and explored selection surfaces through male and female function. The work was carried out in northern Sweden during two flowering seasons (1994 and 1995) in one natural population and one season (1995) in another natural population. Fitness was estimated as number of pollinia removed (male function) and number of fruits produced (female function). We detected directional selection towards larger inflorescence size (flower number) through both sex functions in both populations in 1995. In 1994, with an unusually dry growing season, 78% of the individuals failed to set any fruit, and there was selection for larger inflorescences only through male function. In this year, there was selection towards longer flower spurs, which could be a direct or indirect effect of spurs being shortened by drought. The results demonstrate that selection patterns may vary temporally and spatially, and that the 'male function hypothesis' may be applicable as female function is more resource dependent than male function.     

Direct selection on allozymes is not required to explain heterogeneity among marker loci across a Mytilus hybrid zone

Unequal differentiation between two types of loci (allozyme and DNA markers) across a Mytilus hybrid zone has recently been claimed as evidence for direct selection on some allozyme loci. We provide here a counter-example: a noncoding DNA locus that exhibits as much differentiation as the incriminated allozymes do. The levels of genetic differentiation varied widely among both allozymes and noncoding DNA markers and no clear difference emerged between the two types of markers. This suggests that the strong interlocus variance in genetic differentiation has been confounded with a discrepancy between marker types as a result of an insufficient and unbalanced locus sampling. Heterogeneity in differentiation among neutral loci can be created by stochastic variance during the allopatric divergence preceding a secondary contact. In hybrid zones, a further source of variance is differential introgression among chromosomal regions after the secondary contact owing to the local influence of selected genes on more or less distant markers. However, the degree of differentiation alone gives no way to distinguish indirect pseudo-selection (a regular and ubiquitous feature of hybrid zones) from direct selection. More generally, we suggest that comparative neutrality tests based on discrepancies among marker types have to be applied with caution when the presence of semi-permeable genetic barriers to gene exchange is suspected.     

Dietary constraints on encephalization in primates

Encephalization, and its relationship to potential selective forces, have been a focus of many studies of primate adaptation. It has been argued that gut size may constrain brain mass because these two types of "expensive tissue" (among others) compete in their metabolic requirements (Aiello and Wheeler [1995] Curr. Anthropol. 36:199-221). Following from the inverse correlation of gut size with diet quality, the expensive tissue hypothesis predicts that differences in diet quality are positively correlated with differences in brain mass, once the correlation of each variable with body mass is taken into account. We tested this prediction using both nonphylogenetic and phylogenetic methods. The results of both methods are consistent with predictions made by the expensive tissue hypothesis. We also discuss several examples of independent contrasts that are consistent with the hypothesis (e.g., Colobinae vs. Cercopithecinae), as well as some that are not (e.g., Tarsius vs. anthropoidea). Overall, the results indicate that improved diet quality, by allowing reduction in relative gut mass, is one mechanism involved in increased encephalization.     

Hypothesis testing for the genetic background of quantitative traits

The testing of Bayesian point null hypotheses on variance component models have resulted in a tough assignment for which no clear and generally accepted method exists. In this work we present what we believe is a succeeding approach to such a task. It is based on a simple reparameterization of the model in terms of the total variance and the proportion of the additive genetic variance with respect to it, as well as on the explicit inclusion on the prior probability of a discrete component at origin. The reparameterization was used to bypass an arbitrariness related to the impropriety of uninformative priors onto unbounded variables while the discrete component was necessary to overcome the zero probability assigned to sets of null measure by the usual continuous variable models. The method was tested against computer simulations with appealing results.     

Horizontal gene transfer in microbial genome evolution

Horizontal gene transfer is the collective name for processes that permit the exchange of DNA among organisms of different species. Only recently has it been recognized as a significant contribution to inter-organismal gene exchange. Traditionally, it was thought that microorganisms evolved clonally, passing genes from mother to daughter cells with little or no exchange of DNA among diverse species. Studies of microbial genomes, however, have shown that genomes contain genes that are closely related to a number of different prokaryotes, sometimes to phylogenetically very distantly related ones. (Doolittle et al., 1990, J. Mol. Evol. 31, 383-388; Karlin et al., 1997, J. Bacteriol. 179, 3899-3913; Karlin et al., 1998, Annu. Rev. Genet. 32, 185-225; Lawrence and Ochman, 1998, Proc. Natl. Acad. Sci. USA 95, 9413-9417; Rivera et al., 1998, Proc. Natl. Acad. Sci. USA 95, 6239-6244; Campbell, 2000, Theor. Popul. Biol. 57 71-77; Doolittle, 2000, Sci. Am. 282, 90-95; Ochman and Jones, 2000, Embo. J. 19, 6637-6643; Boucher et al. 2001, Curr. Opin., Microbiol. 4, 285-289; Wang et al., 2001, Mol. Biol. Evol. 18, 792-800). Whereas prokaryotic and eukaryotic evolution was once reconstructed from a single 16S ribosomal RNA (rRNA) gene, the analysis of complete genomes is beginning to yield a different picture of microbial evolution, one that is wrought with the lateral movement of genes across vast phylogenetic distances. (Lane et al., 1988, Methods Enzymol. 167, 138-144; Lake and Rivera, 1996, Proc. Natl. Acad. Sci. USA 91, 2880-2881; Lake et al., 1999, Science 283, 2027-2028).