Phylogeography and population genetics of the maize stalk borer Busseola fusca (Lepidoptera, Noctuidae) in sub-Saharan Africa

The population genetics and phylogeography of African phytophagous insects have received little attention. Some, such as the maize stalk borer Busseola fusca, display significant geographic differences in ecological preferences that may be congruent with patterns of molecular variation. To test this, we collected 307 individuals of this species from maize and cultivated sorghum at 52 localities in West, Central and East Africa during the growing season. For all collected individuals, we sequenced a fragment of the mitochondrial cytochrome b. We tested hypotheses concerning the history and demographic structure of this species. Phylogenetic analyses and nested clade phylogeographic analyses (NCPA) separated the populations into three mitochondrial clades, one from West Africa, and two--Kenya I and Kenya II--from East and Central Africa. The similar nucleotide divergence between clades and nucleotide diversity within clades suggest that they became isolated at about the same time in three different refuges in sub-Saharan Africa and have similar demographic histories. The results of mismatch distribution analyses were consistent with the demographic expansion of these clades. Analysis of molecular variance (amova) indicated a high level of geographic differentiation at different hierarchical levels. NCPA suggested that the observed distribution of haplotypes at several hierarchical levels within the three major clades is best accounted for by restricted gene flow with isolation by distance. The domestication of sorghum and the introduction of maize in Africa had no visible effect on the geographic patterns observed in the B. fusca mitochondrial genome.     

Testing the hypothesis on the relationship between aerodynamic roughness length and albedo using vegetation structure parameters

Surface albedo (α) and aerodynamic roughness length (z ₀), which partition surface net radiation into energy fluxes, are critical land surface properties for biosphere–atmosphere interactions and climate variability. Previous studies suggested that canopy structure parameters influence both α and z ₀; however, no field data have been reported to quantify their relationships. Here, we hypothesize that a functional relationship between α and z ₀ exists for a vegetated surface, since both land surface parameters can be conceptually related to the characteristics of canopy structure. We test this hypothesis by using the observed data collected from 50 site-years of field measurements from sites worldwide covering various vegetated surfaces. On the basis of these data, a negative linear relationship between α and log(z ₀) was found, which is related to the canopy structural parameter. We believe that our finding is a big step toward the estimation of z ₀ with high accuracy. This can be used, for example, in the parameterization of land properties and the observation of z ₀ using satellite remote sensing.     

Molecular cloning and characterization of a novel laccase gene from a white-rot fungus Polyporus grammocephalus TR16 and expression in Pichia pastoris

Aims: To isolate a novel laccase gene from white‐rot fungus Polyporus grammocephalus TR16 and heterologous expression in Pichia pastoris. The characteristics of the heterologously expressed laccase are also studied. Methods and Results: Anchored PCR and 3′ RACE protocol were applied to obtain the full length of the laccase gene, which comprised 12 introns and an opening frame of 1769 bp. The deduced amino acid sequence of the laccase gene had an identity of 45–66% with the laccases reported previously. The cDNA was expressed in Pi. pastoris GS115 with native and α‐factor secretion signal peptides. The laccase activity obtained with the native signal peptide is threefold higher than that obtained with the α‐factor secretion signal peptide. The highest activity of the heterologously expressed laccase reached 893·3 U ml^?1, with its molecular mass estimated to be 65·4 kDa by SDS‐PAGE. The purified heterologously expressed laccase was stable at a pH range of 7·0–10·0. The optimum pH and temperature were 4·5 and 50°C, respectively; the K_m value for ABTS (3‐ethylbenzthiazoline‐6‐sulphonate) was 0·66 mmol l^?1. Conclusion: The novel laccase gene is cloned successfully and heterologously expressed in Pi. pastoris. Significance and Impact of the Study: A novel laccase gene isolated from a tropical fungus serves as a good source for pulp bleaching and wood processing.     

Morphological variation in hybrids between Salmo marmoratus, and alien Salmo species in the Volarja stream, Soca River basin, Slovenia

There were significant correlations between colour pattern, LDH -5*, genotype and certain meristic characters in 59 hybrid trout Salmo , sp. from the Volarja stream, Soca River basin, Slovenia. It is concluded that panmixia between native Salmo marmoratus , and introduced S. trutta , of Atlantic, Danubian and Mediterranean origin had not been reached in this zone, despite the long period of introgression. The result is in agreement with other studies dealing with introgression in Salmo , and for management purposes certain morphological characters, especially colour pattern, can be a valuable tool in restoring the marble trout population in the Soca River.     

Sex‐specific fitness variation in gynodioecious Beta vulgaris ssp. maritima: do empirical observations fit theoretical predictions?

In gynodioecious species, in which hermaphroditic and female plants co-occur, the maintenance of sexual polymorphism relies on the genetic determination of sex and on the relative fitness of the different phenotypes. Flower production, components of male fitness (pollen quantity and pollen quality) and female fitness (fruit and seed set) were measured in gynodioecious Beta vulgaris spp. maritima, in which sex is determined by interactions between cytoplasmic male sterility (CMS) genes and nuclear restorers of male fertility. The results suggested that (i) female had a marginal advantage over hermaphrodites in terms of flower production only, (ii) restored CMS hermaphrodites (carrying both CMS genes and nuclear restorers) suffered a slight decrease in fruit production compared to non-CMS hermaphrodites and (iii) restored CMS hermaphrodites were poor pollen producers compared to non-CMS hermaphrodites, probably as a consequence of complex determination of restoration. These observations potentially have important consequences for the conditions of maintenance of sexual polymorphism in B. vulgaris and are discussed in the light of existing theory on evolutionary dynamics of gynodioecy.     

A role for α-adducin (ADD-1) in nematode and human memory

Identifying molecular mechanisms that underlie learning and memory is one of the major challenges in neuroscience. Taken the advantages of the nematode Caenorhabditis elegans, we investigated α-adducin (add-1) in aversive olfactory associative learning and memory. Loss of add-1 function selectively impaired short- and long-term memory without causing acquisition, sensory, or motor deficits. We showed that α-adducin is required for consolidation of synaptic plasticity, for sustained synaptic increase of AMPA-type glutamate receptor (GLR-1) content and altered GLR-1 turnover dynamics. ADD-1, in a splice-form- and tissue-specific manner, controlled the storage of memories presumably through actin-capping activity. In support of the C. elegans results, genetic variability of the human ADD1 gene was significantly associated with episodic memory performance in healthy young subjects. Finally, human ADD1 expression in nematodes restored loss of C. elegans add-1 gene function. Taken together, our findings support a role for α-adducin in memory from nematodes to humans. Studying the molecular and genetic underpinnings of memory across distinct species may be helpful in the development of novel strategies to treat memory-related diseases.     

Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase

Altered prolyl oligopeptidase (PREP) activity is found in many common neurological and other genetic disorders, and in some cases PREP inhibition may be a promising treatment. The active site of PREP resides in an internal cavity; in addition to the direct interaction between active site and substrate or inhibitor, the pathway to reach the active site (the gating mechanism) must be understood for more rational inhibitor design and understanding PREP function. The gating mechanism of PREP has been investigated through molecular dynamics (MD) simulation combined with crystallographic and mutagenesis studies. The MD results indicate the inter-domain loop structure, comprised of 3 loops at residues, 189-209 (loop A), 577-608 (loop B), and 636-646 (loop C) (porcine PREP numbering), are important components of the gating mechanism. The results from enzyme kinetics of PREP variants also support this hypothesis: When loop A is (1) locked to loop B through a disulphide bridge, all enzyme activity is halted, (2) nicked, enzyme activity is increased, and (3) removed, enzyme activity is only reduced. Limited proteolysis study also supports the hypothesis of a loop A driven gating mechanism. The MD results show a stable network of H-bonds that hold the two protein domains together. Crystallographic study indicates that a set of known PREP inhibitors inhabit a common binding conformation, and this H-bond network is not significantly altered. Thus the domain separation, seen to occur in lower taxa, is not involved in the gating mechanism for mammalian PREP. In two of the MD simulations we observed a conformational change that involved the breaking of the H-bond network holding loops A and B together. We also found that this network was more stable when the active site was occupied, thus decreasing the likelihood of this transition.     

Fraction of informative recombinations: a heuristic approach to analyze recombination rates

In this article we present a new heuristic approach (informative recombinations, InfRec) to analyze recombination density at the sequence level. InfRec is intuitive and easy and combines previously developed methods that (i) resolve genotypes into haplotypes, (ii) estimate the minimum number of recombinations, and (iii) evaluate the fraction of informative recombinations. We tested this approach in its sliding-window version on 117 genes from the SeattleSNPs program, resequenced in 24 African-Americans (AAs) and 23 European-Americans (EAs). We obtained population recombination rate estimates (rho(obs)) of 0.85 and 0.37 kb(-1) in AAs and EAs, respectively. Coalescence simulations indicated that these values account for both the recombinations and the gene conversions in the history of the sample. The intensity of rho(obs) varied considerably along the sequence, revealing the presence of recombination hotspots. Overall, we observed approximately 80% of recombinations in one-third and approximately 50% in only 10% of the sequence. InfRec performance, tested on published simulated and additional experimental data sets, was similar to that of other hotspot detection methods. Fast, intuitive, and visual, InfRec is not constrained by sample size limitations. It facilitates understanding data and provides a simple and flexible tool to analyze recombination intensity along the sequence.     

Increased Quantity and Quality of Coarse Soil Organic Matter Fraction at Elevated CO2 in a Grazed Grassland are a Consequence of Enhanced Root Growth Rate and Turnover

The aims of this study were to determine whether elevated atmospheric CO₂ concentration modifies plant organic matter (OM) fluxes to the soil and whether any change in the fluxes can modify soil OM accumulation. Measurements were made in a grazed temperate grassland after almost 4 years exposure to elevated atmospheric CO₂ (475 μl l^-1) using a Free Air CO₂ Enrichment (FACE) facility located in the North Island of New Zealand. Aboveground herbage biomass and leaf litter production were not altered by elevated CO₂ but root growth rate, as measured with the ingrowth core method, and root turnover were strongly stimulated by elevated CO₂ particularly at low soil moisture contents during summer. Consequently, significantly more plant material was returned to the soil under elevated CO₂ leading to an accumulation of coarse (> 1 mm) particulate organic matter (POM) but not of finer POM fractions. The accumulating POM exhibited a lower C/N ratio, which was attributed to the higher proportion of legumes in the pasture under elevated CO₂. Only small changes were detected in the size and activity of the soil microbial biomass in response to the POM accumulation, suggesting that higher organic substrate availability did not stimulate microbial growth and activity despite the apparent lower C/N ratio of accumulating POM. As a result, elevated CO₂ may well lead to an accumulation of OM in grazed grassland soil in the long term.