Crop Genebanks: Regeneration and Cutorial Load

This nation\u27s crop genetic resources are currently conserved in a se­ries of genebanks and clonal repositories that are part of the National Plant Germplasm System (NPGS). The largest and most complex assemblage of crop germplasm is held at the NPGS genebank in Griffin, Georgia. Curators, who are also technical experts, manage the collections of individual taxa and are responsible for the regeneration, characterization, acquisition, and distribution of those plant materials. The nature of the duties associated with the management of these germplasm collections, specifically their routine regeneration, results in professional challenges for those technical experts engaged in that and similarly nontechnical activities. Various approaches to address this issue including the allocation of resources specifically earmarked for career-enhancing activities of technical professionals, and the clear separation of funding allocated for basic germplasm maintenance activities vs. other activities, are discussed. Also discussed are various means to increase the efficiency of the regeneration process

Pockets of Proterozoic hydrocarbons and implications for the Archaean

Precambrian biomarkers convey invaluable information about the early evolution of life, ancient ecosystems, redox conditions, climate and depositional environment and prospective petroleum systems. They are however thermally unstable, easily obliterated by contamination and thus extremely difficult to find. This is particularly true if conditions favourable for biomarker preservation had to prevail for more than 2.5 billion years – the prerequisite for finding Archaean biomarkers. Many organic geochemists abandoned this hope after original discoveries of Archaean biomarkers proved to be of younger origin [1,2] but our study of ca. 550-825 Ma old sediments from the Centralian Superbasin now shows that biomarkers can be preserved in distinctive pockets in seemingly barren areas, even if sections are metamorphosed in parts. Most Centralian sections seem empty. Yet, eventually we identified intervals with preserved biomarkers in three drill cores. A detailed investigation of 825 Ma sediments in drill core Mt Charlotte-1 revealed maturity variations that are most likely due to hydrothermal influence and in turn control the hydrocarbon preservation. Sediments might appear metamorphosed after localized, subtle alteration by hydrothermal fluids but protected intervals can still contain biomarkers. The same might be true for Archaean sediments and we might still find those protected intervals with indigenous biomarkers that allow us to glimpse the early life on earth

Isolation and characterization of microsatellite markers from Musa balbisiana

This is the first report of targeted development of B genome microsatellite markers in Musa. A total of 44 sequences with microsatellites were isolated from an enriched library of Musa balbisiana cv. 'Tani' (BB genome). Of these, 25 were polymorphic when screened on 14 diverse diploid and triploid Musa accessions. The number of alleles detected by each marker ranged between one and seven. All 25 microsatellite markers generated amplification products in all species and genome complements. These new microsatellite markers fill an important gap for diversity assessment and linkage mapping studies in plantain (AAB) and cooking banana (ABB

"Better Safe than Sorry" - Individual Risk-free Pension Schemes in the European Union - Macroeconomic Benefits, the Mobile Working Citizen's Perspective and Why Nots

Variations between the diverse pension systems in the member states of the European Union hamper labour market mobility, across country borders but also within the countries of the European Union. From a macroeconomic perspective, and in the light of demographic pressure, this paper argues that allowing individual instead of collective pension building would greatly improve labour market flexibility and thus enhance the functioning of the monetary union. I argue that working citizens would benefit, for three reasons, from pension saving in a risk-free savings account. First, citizens would have a clear picture of the accumulation of their own pension savings throughout their working life. Second, they would pay hardly any extra costs and, third, once retired they would not be subject to the whims of government or other pension fund managers. This paper investigates the feasibility of individual pension building under various parameter settings by calculating the pension saved during a working life and the pension dis-saved after retirement. The findings show that there are no reasons why the European Union and individual member states should not allow individual risk-free pension savings accounts. This would have macroeconomic benefits and provide a solid pension provision that can enhance mobility, instead of engaging workers in different mandatory collective pension schemes that exist around in the European Union

Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)

Societal Impact Statement Crop wild relatives—wild species closely related to cultivated plants—are valuable genetic resources for crop improvement, but gaps in knowledge constrain their conservation and limit their further use. We develop new information on the distributions, potential breeding value, and conservation status of the 16 known wild relatives of cultivated pumpkins, squashes, zucchini, and gourds (Cucurbita L.). The taxa occur from the central USA to Central America, plus two South American species, with the greatest richness in central Mexico and the western borderlands between Mexico and the USA. We determine the majority of species are of medium priority for conservation, both with regard to collecting for ex situ maintenance, and for enhanced habitat protection. Summary Crop wild relatives are valuable genetic resources for crop improvement. Knowledge gaps, including with regard to taxonomy, distributions, and characterization for traits of interest constrain their use in plant breeding. These deficiencies also affect conservation planning, both with regard to in situ habitat protection, and further collection of novel diversity for ex situ maintenance. Here we model the potential ranges of all 16 known wild cucurbit taxa (Cucurbita L.), use ecogeographic information to infer their potential adaptations to abiotic stresses, and assess their ex situ and in situ conservation status. The taxa occur from the central USA to Central America, plus two South American species. Predicted taxon richness was highest in central Mexico and in the western borderlands between Mexico and the USA. We find substantial ecogeographic variation both across taxa and among populations within taxa, with regard to low temperatures, high and low precipitation, and other adaptations of potential interest for crop breeding. We categorize 13 of the taxa medium priority for further conservation as a combination of the ex situ and in situ assessments, two low priority, and one sufficiently conserved. Further action across the distributions of the taxa, with emphasis on taxonomic richness hotspots, is needed to comprehensively conserve wild Cucurbita populations

An application of kernel methods to variety identification based on SSR markers genetic fingerprinting

<p>Abstract</p> <p>Background</p> <p>In crop production systems, genetic markers are increasingly used to distinguish individuals within a larger population based on their genetic make-up. Supervised approaches cannot be applied directly to genotyping data due to the specific nature of those data which are neither continuous, nor nominal, nor ordinal but only partially ordered. Therefore, a strategy is needed to encode the polymorphism between samples such that known supervised approaches can be applied. Moreover, finding a minimal set of molecular markers that have optimal ability to discriminate, for example, between given groups of varieties, is important as the genotyping process can be costly in terms of laboratory consumables, labor, and time. This feature selection problem also needs special care due to the specific nature of the data used.</p> <p>Results</p> <p>An approach encoding SSR polymorphisms in a positive definite kernel is presented, which then allows the usage of any kernel supervised method. The polymorphism between the samples is encoded through the Nei-Li genetic distance, which is shown to define a positive definite kernel between the genotyped samples. Additionally, a greedy feature selection algorithm for selecting SSR marker kits is presented to build economical and efficient prediction models for discrimination. The algorithm is a filter method and outperforms other filter methods adapted to this setting. When combined with kernel linear discriminant analysis or kernel principal component analysis followed by linear discriminant analysis, the approach leads to very satisfactory prediction models.</p> <p>Conclusions</p> <p>The main advantage of the approach is to benefit from a flexible way to encode polymorphisms in a kernel and when combined with a feature selection algorithm resulting in a few specific markers, it leads to accurate and economical identification models based on SSR genotyping.</p

Dissecting the impact of environment, season and genotype on blackcurrant fruit quality traits.

This work aims to determine the effect of genotype x environment (GxE) interaction that influence blackcurrant (Ribes nigrum) fruit quality. We applied metabolomics-driven analysis on fruits from four cultivars grown in contrasting European-locations over two seasons. By integrating metabolomics and sensory analysis, we also defined specific metabolic signatures associated with consumer acceptance. Our results showed that rainfall is a crucial factor associated with accumulation of delphinidin- and cyanidin-3-O-glucoside, the two mayor blackcurrant pigments meanwhile temperature affects the main organic acid levels which can be decisive for fruit taste. Sensorial analysis showed that increases in terpenoid and acetate ester volatiles were strongly associated with higher appreciation score, while proacacipetalin, a cyanogenic-glycoside, was positively associated to bitter taste. Our results pave the way for the selection of high-quality cultivars and suitable production sites for blackcurrant cultivation.publishedVersio

Dilute gas of ultracold two-level atoms inside a cavity; generalized Dicke model

We consider a gas of ultracold two-level atoms confined in a cavity, taking into account for atomic center-of-mass motion and cavity mode variations. We use the generalized Dicke model, and analyze separately the cases of a Gaussian, and a standing wave mode shape. Owing to the interplay between external motional energies of the atoms and internal atomic and field energies, the phase-diagrams exhibit novel features not encountered in the standard Dicke model, such as the existence of first and second order phase transitions between normal and superradiant phases. Due to the quantum description of atomic motion, internal and external atomic degrees of freedom are highly correlated leading to modified normal and superradiant phases.Comment: 10 pages, 7 figure

Author Correction: A consensus-based transparency checklist.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Impedance-based phenotypic readout of transporter function: a case for glutamate transporters

Excitatory amino acid transporters (EAAT/SLC1) mediate Na+-dependent uptake of extracellular glutamate and are potential drug targets for neurological disorders. Conventional methods to assess glutamate transport in vitro are based on radiolabels, fluorescent dyes or electrophysiology, which potentially compromise the cell's physiology and are generally less suited for primary drug screens. Here, we describe a novel label-free method to assess human EAAT function in living cells, i.e., without the use of chemical modifications to the substrate or cellular environment. In adherent HEK293 cells overexpressing EAAT1, stimulation with glutamate or aspartate induced cell spreading, which was detected in real-time using an impedance-based biosensor. This change in cell morphology was prevented in the presence of the Na+/K+-ATPase inhibitor ouabain and EAAT inhibitors, which suggests the substrate-induced response was ion-dependent and transporter-specific. A mechanistic explanation for the phenotypic response was substantiated by actin cytoskeleton remodeling and changes in the intracellular levels of the osmolyte taurine, which suggests that the response involves cell swelling. In addition, substrate-induced cellular responses were observed for cells expressing other EAAT subtypes, as well as in a breast cancer cell line (MDA-MB-468) with endogenous EAAT1 expression. These findings allowed the development of a label-free high-throughput screening assay, which could be beneficial in early drug discovery for EAATs and holds potential for the study of other transport proteins that modulate cell shape.Medicinal Chemistr