Participatory plant breeding: a way to arrive at better-adapted onion varieties

The search for varieties that are better adapted to organic farming is a current topic in the organic sector. Breeding programmes specific for organic agriculture should solve this problem. Collaborating with organic farmers in such programmes, particularly in the selection process, can potentially result in varieties better adapted to their needs. Here, we assume that organic farmers' perceptive of plant health is broader than that of conventional breeders. Two organic onion farmers and one conventional onion breeder were monitored in their selection activities in 2004 and 2005 in order to verify whether and in which way this broader view on plant health contributes to improvement of organic varieties. They made selections by positive mass selection in three segregating populations under organic conditions. The monitoring showed that the organic farmers selected in the field for earliness and downy mildew and after storage for bulb characteristics. The conventional breeder selected only after storage. Farmers and breeder applied identical selection directions for bulb traits as a round shape, better hardness and skin firmness. This resulted in smaller bulbs in the breeders’ populations, while the bulbs in the farmer populations were bigger than in the original population. In 2006 and 2007 the new onion populations will be compared with each other and the original populations to determine the selection response

Hydrogen bonding of nitroxide spin labels in membrane proteins

On the basis of experiments at 275 GHz, we reconsider the dependence of the continuous-wave EPR spectra of nitroxide spin-labeled protein sites in sensory- and bacteriorhodopsin on the micro-environment. The high magnetic field provides the resolution necessary to disentangle the effects of hydrogen bonding and polarity. In the gxx region of the 275 GHz EPR spectrum, bands are resolved that derive from spin-label populations carrying no, one or two hydrogen bonds. The gxx value of each population varies hardly from site to site, significantly less than deduced previously from studies at lower microwave frequencies. The fractions of the populations vary strongly, which provides a consistent description of the variation of the average gxx and the average nitrogen-hyperfine interaction Azz from site to site. These variations reflect the difference in the proticity of the micro-environment, and differences in polarity contribute marginally. Concomitant W-band ELDOR- detected NMR experiments on the corresponding nitroxide in perdeuterated water resolve population-specific nitrogen-hyperfine bands, which underlies the interpretation for the proteins

Simulation and optimisation of terahertz emission from InGaAs and InP photoconductive switches

We simulate the terahertz emission from laterally-biased InGaAs and InP using a three-dimensional carrier dynamics model in order to optimise the semiconductor material. Incident pump-pulse parameters of current Ti:Sapphire and Er:fibre lasers are chosen, and the simulation models the semiconductor's bandstructure using parabolic Gamma, L and X valleys, and heavy holes. The emitted terahertz radiation is propagated within the semiconductor and into free space using a model based on the Drude-Lorentz dielectric function. As the InGaAs alloy approaches InAs an increase in the emitted power is observed, and this is attributed to a greater electron mobility. Additionally, low-temperature grown and ion-implanted InGaAs are modelled using a finite carrier trapping time. At sub-picosecond trapping times the terahertz bandwidth is found to increase significantly at the cost of a reduced emission power.Comment: 9 pages, 7 figure

A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour

High‐density SNP microarrays (“SNP chips”) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high‐density Affymetrix Axiom chip with around 500,000 SNP s, designed to perform genomics studies of great tit (Parus major ) populations. We demonstrate that the per‐SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB ), a personality trait that has been widely studied in great tits and other species. No SNP s reached genomewide significance, including at DRD 4 , a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNP s previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNP s by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates

A genetic linkage map of Sole (Solea solea): A tool for evolutionary and comparative analyses of exploited (flat)fishes

Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L.) is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes), Nile tilapia (Oreochromis niloticus), three-spined stickleback (Gasterosteus aculeatus) and green spotted pufferfish (Tetraodon nigroviridis). This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus), another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one) a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species

A comparison of electrochemical degradation of phenol on boron doped diamond and lead dioxide anodes

This work compares two electrode materials used to mineralize phenol contained in waste waters. Two disks covered with either boron doped diamond (BDD) or PbO2 were used as anodes in a one compartment flow cell under the same hydrodynamic conditions. Efficiencies of galvanostatic electrolyses are compared on the basis of measurements of Total Organic Carbon (TOC) and Chemical Oxygen Demand (COD). Galvanostatic electrolyses were monitored by analysis of phenol and of its oxidation derivatives to evaluate the operating time needed for complete elimination of toxic aromatics. The experimental current efficiency is close to the theoretical value for the BDD electrode. Other parameters being equal, phenol species disappeared at the same rate using the two electrode materials but the BDD anode showed better efficiency to eliminate TOC and COD. Moreover, during the electrolysis less intermediates are formed with BDD compared to PbO2 whatever the current density. A comparison of energy consumption is given based on the criterion of 99% removal of aromatic compounds

Electrochemical synthesis of peroxomonophosphate using boron-doped diamond anodes

A new method for the synthesis of peroxomonophosphate, based on the use of boron-doped diamond electrodes, is described. The amount of oxidant electrogenerated depends on the characteristics of the supporting media (pH and solute concentration) and on the operating conditions (temperature and current density). Results show that the pH, between values of 1 and 5, does not influence either the electrosynthesis of peroxomonophosphate or the chemical stability of the oxidant generated. Conversely, low temperatures are required during the electrosynthesis process to minimize the thermal decomposition of peroxomonophosphate and to guarantee significant oxidant concentration. In addition, a marked influence of both the current density and the initial substrate is observed. This observation can be explained in terms of the contribution of hydroxyl radicals in the oxidation mechanisms that occur on diamond surfaces. In the assays carried out below the water oxidation potential, the generation of hydroxyl radicals did not take place. In these cases, peroxomonophosphate generation occurs through a direct electron transfer and, therefore, at these low current densities lower concentrations are obtained. On the other hand, at higher potentials both direct and hydroxyl radical-mediated mechanisms contribute to the oxidant generation and the process is more efficient. In the same way, the contribution of hydroxyl radicals may also help to explain the significant influence of the substrate concentration. Thus, the coexistence of both phosphate and hydroxyl radicals is required to ensure the generation of significant amounts of peroxomonophosphoric acid

Heterodimeric Analogues of the Potent Y1R Antagonist 1229U91, Lacking One of the Pharmacophoric C-Terminal Structures, Retain Potent Y1R Affinity and Show Improved Selectivity over Y4R

The cyclic dimeric peptide 1229U91 (GR231118) has an unusual structure and displays potent, insurmountable antagonism of the Y1 receptor. To probe the structural basis for this activity, we have prepared ring size variants and heterodimeric compounds, identifying the specific residues underpinning the mechanism of 1229U91 binding. The homodimeric structure was shown to be dispensible, with analogues lacking key pharmacophoric residues in one dimer arm retaining high antagonist affinity. Compounds 11d-h also showed enhanced Y1R selectivity over Y4R compared to 1229U91

Optically pure, structural and fluorescent analogues of a dimeric Y4 receptor agonist derived by an olefin metathesis approach

The dimeric peptide 1 (BVD-74D, as a diastereomeric mixture) is a potent and selective Neuropeptide Y Y4 receptor agonist. It represents a valuable candidate in developing traceable ligands for pharmacological studies of Y4 receptors, and as a lead compound for anti-obesity drugs. Its optically pure stereoisomers along with analogues and fluorescently labelled variants were prepared by exploiting alkene metathesis reactions. The (2R,7R)- diaminosuberoyl containing peptide, (R,R)-1 had markedly higher affinity and agonist efficacy than its (S,S)-counterpart. Furthermore the sulfo-Cy5 labelled (R,R)-14 retained high agonist potency as a novel fluorescent ligand for imaging Y4 receptors

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation