Ppe.CR.1 DNA test for predicting chilling requirement in peach.

Chilling requirement (CR) is an important agronomic trait controlling the floral bud break for proper flowering in peach. Even though it has been widely researched and several peach CR quantitative trait loci (QTLs) have been identified, no diagnostic DNA tests validated in the U.S. peach breeding germplasm are available for this trait. Breeders and growers need a simple DNA test to predict the CR of peach cultivars for their particular environment. Therefore, we developed a quick and reliable Kompetitive Allele Specific PCR (KASP) DNA test using haplotype information from 9K IPSC genotype data of the U.S. peach germplasm integrating four CR-associated SNP markers from the previously reported CR QTL region on linkage group 1. Four KASP assays (Ppe.CR.1-1 to -4) were developed and validated on 77 peach cultivars, and nine accessions from two F2 populations, with 96 and 74% accuracy in determining expected CR genotype (compared to SNP array) and predicting phenotype, respectively. Furthermore, the Ppe.CR.1 showed 80% accuracy in predicting the precise CR phenotype in the Clemson University peach breeding material. Only one Ppe.CR.1 KASP assay (Ppe.CR.1-1) is needed to distinguish between haplotypes with CR lower and higher than 800 chilling hours, and two Ppe.CR.1 assays (Pp.CR.1-1 and -4), are capable of distinguishing low, moderate, and high CR alleles. Coupled with the crude DNA extraction, the Ppe.CR.1 DNA test provides a low-cost option for breeders and growers to predict CR in peach material with more than 70% accuracy.

Horizon scan of global conservation issues for 2011.

This review describes outcomes of a 2010 horizon-scanning exercise building upon the first exercise conducted in 2009. The aim of both horizon scans was to identify emerging issues that could have substantial impacts on the conservation of biological diversity, and to do so sufficiently early to encourage policy-relevant, practical research on those issues. Our group included professional horizon scanners and researchers affiliated with universities and non- and inter-governmental organizations, including specialists on topics such as invasive species, wildlife diseases and coral reefs. We identified 15 nascent issues, including new greenhouse gases, genetic techniques to eradicate mosquitoes, milk consumption in Asia and societal pessimism.

Structural characterization of alpha-zein.

A variety of published physical measurements, computational algorithms, and structural modeling methods have been used to create a molecular model of 19 kDa alpha-zein (Z19). Zetaeins are water-insoluble storage proteins found in corn protein bodies. Analyses of the protein sequence using probability algorithms, structural studies by circular dichroism, infrared spectroscopy, small-angle X-ray scattering (SAXS), light scattering, proton exchange, NMR, and optical rotatory dispersion experiments suggest that Z19 has approximately 35-60% helical character, made up of nine helical segments of about 20 amino acids with glutamine-rich "turns" or "loops". SAXS and light-scattering experiments suggest that in alcohol/water mixtures alpha-zein exists as an oblong structure with an axial ratio of approximately 6:1. Furthermore, ultracentifugation, birefringence, dielectric, and viscosity studies indicate that alpha-zein behaves as an asymmetric particle with an axial ratio of from 7:1 to 28:1. Published models of alpha-zein to date have not been consistent with the experimental data, and for this reason the structure was re-examined using molecular mechanics and dynamics simulations creating a new three-dimensional (3D) structure for Z19. From the amino acid sequence and probability algorithms this analysis suggested that alpha-zein has coiled-coil tendencies resulting in alpha-helices with about four residues per turn in the central helical sections with the nonpolar residue side chains forming a hydrophobic face inside a triple superhelix. The nine helical segments of the 19 kDa protein were modeled into three sets of three interacting coiled-coil helices with segments positioned end to end. The resulting structure lengthens with the addition of the N- and C-terminal sections, to give an axial ratio of approximately 6 or 7:1 in agreement with recent experiments. The natural carotenoid, lutein, is found to fit into the core of the triple-helical segments and help stabilize the configuration. Molecular dynamics simulations with explicit methanol/water molecules as solvent have been carried out to refine the 3D structure.

Rheological studies utilizing various lots of zein in N,N-dimethylformamide solutions.

Rheological studies were carried out on solutions of zein in N,N-dimethylformamide (DMF), where the specific lot of zein, concentration, time, and temperature were varied. DMF is a good solvent for zein, giving clear, relatively low viscosity solutions. It was found that all of the zein solutions behaved in a non-Newtonian fashion. At high concentration and elevated temperature, zein solutions will increase in viscosity with time. A temperature study on the rate of viscosity rise illustrated that at temperatures above 40 degrees C, the rate of viscosity rise increased in a non-Arrhenius fashion. There can be significant lot to lot variations in commercially obtained zein that gives rise to differences in viscosity and rate of viscosity rises. With the samples studied, viscosity was found to double from one lot of zein to another. Size exclusion chromatography suggests that compositional differences between the lots drive the observed differences in viscosity.

Protease inhibitor phenotypes and serum alpha-1-antitrypsin levels in patients with COPD: a study from Hong Kong.

OBJECTIVE: Many studies have suggested that an imbalance of protease activation and inhibition might result in COPD with emphysema. Levels of alpha-1-antitrypsin (alpha1-AT), the key protease inhibitor, are genetically determined by alleles that present in many phenotypes/subtypes, some of which are associated with deficiency of the protein. We prospectively evaluated the prevalence of the protease inhibitor (Pi) alleles and phenotypes together with the serum alpha1-AT levels in Chinese patients with COPD. METHODOLOGY: The study population comprised 356 patients with COPD. The male-to-female ratio was 4 : 1 with a mean age of 72.4 years (range 44-93 years). Isoelectric focusing was used for Pi phenotyping/subtyping. The frequencies of Pi alleles and phenotypes were compared with the frequencies in 1085 healthy unrelated Chinese control subjects. The serum alpha1-AT levels were measured by the Cobas Fara assay. RESULTS: PiZ was not detected. No significant difference in distribution of PiM phenotypes/subtypes between patients with COPD and healthy controls was observed, except for M1M3 and M2M3. There was also a significant difference in the proportion of variant S and F alleles between the disease group and the control population. CONCLUSION: The low prevalence of deficiency Pi phenotypes/subtypes suggests a lack of contribution of alpha1-AT deficiency to the pathogenesis of COPD in Chinese patients. The strategy of launching an alpha1-AT deficiency detection program among COPD patients, based on the recommendation of the World Health Organization, may not be readily applicable in our local setting.

Is the increased vigour of invasive weeds explained by a trade-off between growth and herbivore resistance?

Blossey and Nötzold (1995) recently hypothesised that the increased vigour of certain invasive plant species has been at the expense of defences against natural enemies. A prediction of their evolution of increased competitive ability (EICA) hypothesis is that invasive genotypes are relatively poorly defended. We tested this prediction with herbivore bioassays and with direct quantification of plant secondary metabolites comparing non-indigenous genotypes of Lythrum salicaria L. (purple loosestrife) with indigenous forms. The herbivore bioassays revealed no significant intra-specific variation in herbivore resistance between indigenous and non-indigenous hosts. The phenolic content of L. salicaria leaves was significantly higher in indigenous genotypes, as predicted by the EICA hypothesis. The average phenolic content of leaves (regardless of their origin) was, however, low, implying that the role of plant phenolics in purple loosestrife anti-herbivore defence is probably limited. It is suggested that the EICA hypothesis, as tested in the current study, does not explain the increased vigour of L. salicaria in non-indigenous habitats.

The small-scale spatial distribution of an invading moth.

We studied the spread of a small leaf-mining moth [Phyllonorycter leucographella (Zeller), Gracillariidae] after its accidental introduction into the British Isles. At large geographical scales, previous work had shown the spread to be well described by a travelling weve of constant velocity. Here, we report the pattern of spread at scales of 1 km2. By locating all bushes of the insect's foodplant (Pyracantha spp.) within 1-km2 quadrats, the precise pattern of colonisation at finer spatial scales could be established. Where the 1-km2 site was colonised by moths from the main advancing front, no spatial pattern in the order that bushes were infested was found. If the source of colonisation was a single or small group of infested plants within the site, there was some evidence that nearby plants were colonised first. We found no evidence of population turnover after colonisation. We interpret the results in terms of a two-stage model of invasion that produces different patterns at small and large geographical scales.

Latitudinal gradients in butterfly body sizes: is there a general pattern?

We tested for the existence of latitudinal gradients in the body sizes of butterflies in North America, Europe, Australia and the Afrotropics. We initially compared body sizes (measured as male forewing length) of all butterflies found in 5° latitudinal bands in each region, and then evaluated the relationship between body size and latitude statistically using the latitudinal midpoint of each species' distribution. Trends were examined for species in all butterfly families together and for each family separately. We found that gradients in body sizes were inconsistent in different geographical regions and butterfly families; in some cases species were larger towards the tropics, in some they were smaller, and in other cases there were no relationships. Most of the gradients, when they existed, reflected between-family effects arising from changes in the relative numbers of species in each family across regions. We conclude that general ecological explanations for geographical trends in butterfly body sizes are inappropriate, and gradients largely reflect historical patterns of speciation within and between taxa in each biogeographical realm. Thus, the robustness of body size gradients found in other insect groups should be confirmed in future studies by including more than one geographical region whenever possible.

The effect of earthworms and snails in a simple plant community.

Snails and earthworms affected the dynamics of a simple, three-species plant community, in the Ecotron controlled environment facility. Earthworms enhanced the establishment, growth and cover of the legume Trifolium dubium, both via the soil and interactions with other plant species. Worms increased soil phosphates, increased root nodulation in T. dubium, and enabled T. dubium seedlings to establish in the presence of grass (Poa annua) litter, by increasing soil heterogeneity. Worms also buried the seeds of Poa annua and Senecio vulgaris, reducing the germination of new seedlings. Snails reduced nitrogen-fixing Trifolium dubium and increased cover of plant litter, thereby reducing ammonia-nitrogen concentrations in the soil. These effects and their interactions demonstrate that the detritivore food chain, and earthworms in particular, cannot be ignored if we are to understand the spatial and temporal dynamics of plant communities.

Latitudinal patterns in European ant assemblages: variation in species richness and body size.

Using published distributions of 65 species from the British Isles and northern Europe, we show that ant assemblages change with latitude in two ways. First, as commonly found for many types of organisms, the number of ant species decreased significantly with increasing latitude. For Ireland and Great Britain, species richness also increased significantly with region area. Second, although rarely demonstrated for ectotherms, the body size of ant species, as measured by worker length, increased significantly with increasing latitude. We found that this body-size pattern existed in the subfamily Formicinae and, to a lesser extent, in the Myrmicinae, which together comprised 95% of the ant species in our study area. There was a trend for formicines to increase in size with latitude faster than myrmicines. We also show that the pattern of increasing body size was due primarily to the ranges of ant species shifting to higher latitudes as their body sizes increased, with larger formicines becoming less represented at southerly latitudes and larger myrmicines becoming more represented at northerly latitudes. We conclude by discussing five potential mechanisms for generating the observed body-size patterns: the heat-conservation hypothesis, two hypotheses concerning phylogenetic history, the migration-ability hypothesis, and the starvation-resistance hypothesis.

Extrinsic vs. intrinsic food shortage and the strength of feeding links: effects of density and food availability on feeding rate of Hyphydrus ovatus.

We use field and laboratory experiments to determine whether Hyphydrus ovatus, a predatory aquatic beetle, is food limited, and whether any food shortage results from depletion of prey by these predators (intrinsic food shortage) or is independent of predation by these beetles (extrinsic food shortage). In the laboratory, differences in feeding rate influence body fat content, thus making fat content a useful index of recent feeding history. H. ovatus collected during the breeding season have fat contents significantly greater than those of H. ovatus starved for 25 days, but not significantly different from those of H. ovatus fed ad libitum for 25 days, indicating that natural feeding rates are near the maximum possible. H. ovatus confined at a density 60 times greater than natural show reduced fat content and feeding rate relative to natural, indicating that at very high densities H. ovatus is capable of depleting its prey. Addition of supplemental natural prey (primarily Cladocera) to experimental enclosures resulted in an order of magnitude increase in prey availability, and a significant increase in fat content and feeding rate of confined H. ovatus. Adults of this species do not appear to be food limited during the breeding season, and extraordinarily high densities of adults seem to be necessary to produce intrinsic food shortage. These results suggest that feeding links between H. ovatus an its principal prey do not have major effects on population dynamics under typical field conditions, and call into question the assumption that closely coupled predator-prey interactions are the sole explanation for observed food-web patterns.