The effects of mispair and nonpair correction in hybrid DNA on base ratios (G + C content) and total amounts of DNA

Base ratios and total DNA amounts can vary substantially between and within higher taxa and genera, and even within species. Gene conversion is one of several mechanisms that could cause such changes. For base substitutions, disparity in conversion direction is accompanied by an equivalent disparity in base ratio at the heterozygous site. Disparity in the direction of gene conversion at meiosis is common and can be extreme. For transitions (which give purine [R]/pyrimidine [Y] mispairs) and for transversions giving unlike R/R and Y/Y mispairs in hybrid DNA, this disparity could give slow but systematic changes in G + C percentage. For transversions giving like R/R and Y/Y mispairs, it could change AT/TA and CG/GC ratios. From the extent of correction direction disparity, one can deduce properties of repair enzymes, such as the ability (1) to excise preferentially the purine from one mispair and the pyrimidine from the other for two different R/Y mispairs from a single heterozygous site and (2) to excise one base preferentially from unlike R/R or Y/Y mispairs. Frame-shifts usually show strong disparity in conversion direction, with preferential cutting of the nonlooped or the looped-out strand of the nonpair in heterozygous h-DNA. The opposite directions of disparity for frame-shifts and their intragenic suppressors as Ascobolus suggest that repair enzymes have a strong, systematic bias as to which strand is cut. The conversion spectra of mutations induced with different mutagens suggest that the nonlooped strand is preferentially cut, so that base additions generally convert to mutant and deletions generally convert to wild-type forms. Especially in nonfunctional or noncoding DNA, this could cause a general increase in DNA amounts. Conversion disparity, selection, mutation, and other processes interact, affecting rates of change in base ratios and total DNA.      

Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red‐listed grasshopper

Inferring the processes underlying spatial patterns of genomic variation is fundamental to understand how organisms interact with landscape heterogeneity and to identify the factors determining species distributional shifts. Here, we use genomic data (restriction site‐associated DNA sequencing) to test biologically informed models representing historical and contemporary demographic scenarios of population connectivity for the Iberian cross‐backed grasshopper Dociostaurus hispanicus, a species with a narrow distribution that currently forms highly fragmented populations. All models incorporated biological aspects of the focal taxon that could hypothetically impact its geographical patterns of genomic variation, including (a) spatial configuration of impassable barriers to dispersal defined by topographic landscapes not occupied by the species; (b) distributional shifts resulting from the interaction between the species bioclimatic envelope and Pleistocene glacial cycles; and (c) contemporary distribution of suitable habitats after extensive land clearing for agriculture. Spatiotemporally explicit simulations under different scenarios considering these aspects and statistical evaluation of competing models within an Approximate Bayesian Computation framework supported spatial configuration of topographic barriers to dispersal and human‐driven habitat fragmentation as the main factors explaining the geographical distribution of genomic variation in the species, with no apparent impact of hypothetical distributional shifts linked to Pleistocene climatic oscillations. Collectively, this study supports that both historical (i.e., topographic barriers) and contemporary (i.e., anthropogenic habitat fragmentation) aspects of landscape composition have shaped major axes of genomic variation in the studied species and emphasizes the potential of model‐based approaches to gain insights into the temporal scale at which different processes impact the demography of natural populations.     

Physiological response of Colorado potato beetle and beet armyworm larvae to depletion of wound-inducible proteinase inhibitors in transgenic potato plants

Larvae of Colorado potato beetle (CPB), Leptinotarsa decemlineata, and beet armyworm (BAW), Spodoptera exigua, reared on potato plants in which wound-induced accumulation of proteinase inhibitors (PIs) was largely reduced through antisense-mediated depletion of a specific lipoxygenase (LOX H3) had significantly larger weight gains than those fed on non-transformed plants. The midgut endoproteolytic activities of CPB larvae fed on non-transformed potato were significantly higher than those from larvae fed on LOX-H3-deficient plants. However, none of these proteolytic activities was inhibited by potato leaf extracts, regardless of the plant that they were fed on. Taken together, these data suggest that CPB, a leaf-feeding specialist of solanaceous plants, is largely adapted to the inducible PIs of potato, though the metabolic cost associated with the hyperproduction of digestive proteases may account for the 14-31% lower weight gain of larvae fed on non-transformed plants. The effect of LOX-H3 depletion on insect performance was more evident with larvae of the polyphagous BAW (52-63% higher weight gain and 73% higher fecundity when reared on LOX-H3-deficient plants). The poorer larval performance of BAW on non-transformed plants may be due to the susceptibility to inhibition by potato leaf tissues of most BAW digestive proteases. Indeed, BAW larvae fed on non-transformed potato showed a significant reduction in most endoproteolytic activities compared to larvae fed on LOX-H3-deficient plants, suggesting a that these insects deal poorly with induced plant defences in potato.     

The membrane M protein carboxy terminus binds to transmissible gastroenteritis coronavirus core and contributes to core stability

The architecture of transmissible gastroenteritis coronavirus includes three different structural levels, the envelope, an internal core, and the nucleocapsid that is released when the core is disrupted. Starting from purified virions, core structures have been reproducibly isolated as independent entities. The cores were stabilized at basic pH and by the presence of divalent cations, with Mg(2+) ions more effectively contributing to core stability. Core structures showed high resistance to different concentrations of detergents, reducing agents, and urea and low concentrations of monovalent ions (<200 mM). Cores were composed of the nucleoprotein, RNA, and the C domain of the membrane (M) protein. At high salt concentrations (200 to 300 mM), the M protein was no longer associated with the nucleocapsid, which resulted in destruction of the core structure. A specific ionic interaction between the M protein carboxy terminus and the nucleocapsid was demonstrated using three complementary approaches: (i) a binding assay performed between a collection of M protein amino acid substitution or deletion mutants and purified nucleocapsids that led to the identification of a 16-amino-acid (aa) domain (aa 237 to 252) as being responsible for binding the M protein to the nucleocapsid; (ii) the specific inhibition of this binding by monoclonal antibodies (MAbs) binding to a carboxy-terminal M protein domain close to the indicated peptide but not by MAbs specific for the M protein amino terminus; and (iii) a 26-residue peptide, including the predicted sequence (aa 237 to 252), which specifically inhibited the binding. Direct binding of the M protein to the nucleoprotein was predicted, since degradation of the exposed RNA by RNase treatment did not affect the binding. It is proposed that the M protein is embedded within the virus membrane and that the C region, exposed to the interior face of the virion in a population of these molecules, interacts with the nucleocapsid to which it is anchored, forming the core. Only the C region of the M protein is part of the core.     

Effects of ajugarins and related neoclerodane diterpenoids on feeding behaviour of Leptinotarsa decemlineata and Spodoptera exigua larvae

Three naturally occurring ajugarins and seven semisynthetic derivatives of them, possessing different functionalities in the decalin part, together with two natural furoneoclerodane diterpenes, have been assessed as feeding behavior modifying agents of larvae of the generalist Spodoptera exigua and a specialist like Leptinotarsa decemlineata. Ajugarin I and some of its derivatives exhibited a significant antifeedant activity against larvae of S. exigua in both choice and no-choice assays. Conversely, the furoneoclerodane diterpenes only presented antifeedant activity against larvae of L. decemlineata. These results indicate that the biological action of the tested substances is strongly modulated by minimal structural variations, which are also responsible for the specificity of action.     

Proteolytic activities in body and faecal extracts of the storage mite, Acarus farris

Trypsin, chymotrypsin, cathepsins B and D, aminopeptidase and carboxypeptidases A and B were detected in body extracts of the storage mite Acarus farris (Oudemans) (Astigmata: Acaridae). Faeces-enriched medium exhibited higher (10-50-fold) specific protease activity rates than those measured with mite body extracts for trypsin, chymotrypsin and carboxypeptidases A and B, suggesting that they are involved in mite digestion. However, the activity of cathepsin B was only three-fold higher in faecal than in body extracts, indicating that its presence in the lumen of the digestive tract is low compared to that of serine proteases. The activity of aminopeptidases was higher in mite bodies, indicating that they might be membrane bound. Cathepsin D activity was only detected in body extracts, indicating that this enzyme is not a digestive protease in this species. Zymograms resolved three major bands of gelatinolytic activity, but at least one protease form was only present in body extracts. Protease inhibitors of different specificity were tested in vivo to establish their potential as control agents. The development of A. farris was significantly retarded when the immature stages were fed on artificial diet containing inhibitors of serine and cysteine proteases and aminopeptidases, whereas no such effect was found with inhibitors of aspartyl proteases and carboxypeptidases. Interestingly, the most significant effects on A. farris occurred when a combination of inhibitors targeting different enzyme classes was supplied mixed in the diet, suggesting a synergistic toxicity. Several plant lectins were also tested, but only wheat germ agglutinin and concanavalin-A affected development.     

Generation of a replication-competent,propagation-deficient virus vector based on the transmissible gastroenteritis coronavirus genome

Replication-competent propagation-deficient virus vectors based on the transmissible gastroenteritis coronavirus (TGEV) genome that are deficient in the essential E gene have been developed by complementation within E(+) packaging cell lines. Cell lines expressing the TGEV E protein were established using the noncytopathic Sindbis virus replicon pSINrep21. In addition, cell lines stably expressing the E gene under the CMV promoter have been developed. The Sindbis replicon vector and the ectopic TGEV E protein did not interfere with the rescue of infectious TGEV from full-length cDNA. Recombinant TGEV deficient in the nonessential 3a and 3b genes and the essential E gene (rTGEV-Delta3abDeltaE) was successfully rescued in these cell lines. rTGEV-Delta3abDeltaE reached high titers (10(7) PFU/ml) in baby hamster kidney cells expressing porcine aminopeptidase N (BHK-pAPN), the cellular receptor for TGEV, using Sindbis replicon and reached titers up to 5 x 10(5) PFU/ml in cells stably expressing E protein under the control of the CMV promoter. The virus titers were proportional to the E protein expression level. The rTGEV-Delta3abDeltaE virions produced in the packaging cell line showed the same morphology and stability under different pHs and temperatures as virus derived from the full-length rTGEV genome, although a delay in virus assembly was observed by electron microscopy and virus titration in the complementation system in relation to the wild-type virus. These viruses were stably grown for >10 passages in the E(+) packaging cell lines. The availability of packaging cell lines will significantly facilitate the production of safe TGEV-derived vectors for vaccination and possibly gene therapy.     

Integrating ecological and genetic structure to define management units for caribou in Eastern Canada

Genetic diversity is a key parameter to delineate management units, but many organisms also display ecological characteristics that may reflect potential local adaptations. Here, we used ecological and genetic information to delineate management units for a complex system involving several ecotypes of caribou (Rangifer tarandus) from Québec and Labrador, eastern Canada. We genotyped 560 caribou at 16 microsatellite loci and used three Bayesian clustering methods to spatially delineate and characterize genetic structure across the landscape. The different approaches employed did not converge on the same solution, and differed in the number of inferred genetic clusters that best fit the dataset but also in the spatial distribution of genetic variation. We reconciled variability among the methods using a synthetic approach that considers the sum of the partitions obtained by each of them and retrieved six genetically distinct groups that differ in their spatial extent across the range of caribou in the study area. These genetic groups are not consistent with the presently defined ecological designations for this species. Combining both genetic and ecological criteria, we distinguished eight independent management units. Overall, the management units we propose should be the focus of conservation and management actions aimed to maximize genetic and ecological diversity and ensure the persistence of caribou populations inhabiting increasingly disturbed landscapes.     

Characteristics of loci and individuals are associated with germline microsatellite mutation rates in lesser kestrels (Falco naumanni)

Although microsatellites are one of the most popular tools in genetic studies, their mutational dynamics and evolution remain unclear. Here, we apply extensive pedigree genotyping to identify and analyze the patterns and factors associated with de novo germline mutations across nine microsatellite loci in a wild population of lesser kestrels (Falco naumanni). A total of 10 germline mutations events were unambiguously identified in four loci, yielding an average mutation rate of 2.96x10(-3). Across loci, mutation rate was positively correlated with locus variability and average allele size. Mutations were primarily compatible with a stepwise mutation model, although not exclusively involved single-step changes. Unexpectedly, we found an excess of maternally transmitted mutations (male-to-female ratio of 0.1). One of the analyzed loci (Fn2.14) resulted hypermutable (mutation rate=0.87%). This locus showed a size-dependent mutation bias, with longer alleles displaying deletions or additions of a small number of repeat than shorter alleles. Mutation probability at Fn2.14 was higher for females and increased with parental (maternal) age but was not associated with individual physical condition, multilocus heterozygosity, allele length or allele span. Overall, our results do not support the male-biased mutation rate described in other organisms and suggest that mutation dynamics at microsatellite loci are a complex process which requires further research.