Twelve years of assessing the quality of preimplantation genetic testing for monogenic disorders

Objective

Genomics Quality Assessment has provided external quality assessments (EQAs) for preimplantation genetic testing (PGT) for 12 years for eight monogenic diseases to identify sub-optimal PGT strategies, testing and reporting of results, which can be shared with the genomics community to aid optimised standards of PGT services for couples.

Method

The EQAs were provided in two stages to mimic end-to-end protocols. Stage 1 involved DNA feasibility testing of a couple undergoing PGT and affected proband. Participants were required to report genotyping results and outline their embryo testing strategy. Lymphoblasts were distributed for mock embryo testing for stage 2. Submitted clinical reports and haplotyping results were assessed against peer-ratified criteria. Performance was monitored to identify poor performance.

Results

The most common testing methodology was short tandem repeat linkage analysis (59%); however, the adoption of single nucleotide polymorphism-based platforms was observed and a move from blastomere to trophectoderm testing. There was a variation in testing strategies, assigning marker informativity and understanding test limitations, some clinically unsafe. Critical errors were reported for genotyping and interpretation.

Conclusion

EQA provides an overview of the standard of preimplantation genetic testing-M clinical testing and identifies areas of improvement for accurate detection of high-risk embryos.     

土壤中嗪草酮迁移和降解的研究

 通过两季马铃薯大田试验，研究了嗪草酮在灌溉沙壤土中的消失和移动情况。结果表明，表层土壤中，嗪草酮施用后最初7～15天内其含量急剧降低，此后随时间推移降低幅度平缓，1993年和1994年试验结束时的残留量分别为5.9μg/kg和2.3μg/kg。两年共采集的379个土样（分布在15～75cm各土层）中只有5个检测到有嗪草酮。1994年大田135cm土层处的水样中，嗪草酮的检测率高达66％，检测浓度范围为0.06～15.85μg/kg，平均浓度为1.94μg/kg。相比较，嗪草酮在大田试验中的消失速率远大于实验室控制条件下的降解速率。     

Individual consistency in exploratory behaviour and mating tactics in male guppies

While behavioural plasticity is considered an adaptation to fluctuating social and environmental conditions, many animals also display a high level of individual consistency in their behaviour over time or across contexts (generally termed ‘personality’). However, studies of animal personalities that include sexual behaviour, or functionally distinct but correlated traits, are relatively scarce. In this study, we tested for individual behavioural consistency in courtship and exploratory behaviour in male guppies (Poecilia reticulata) in two light environments (high vs. low light intensity). Based on previous work on guppies, we predicted that males would modify their behaviour from sneak mating tactics to courtship displays under low light conditions, but also that the rank orders of courtship effort would remain unchanged (i.e. highly sexually active individuals would display relatively high levels of courtship under both light regimes). We also tested for correlations between courtship and exploratory behaviour, predicting that males that had high display rates would also be more likely to approach a novel object. Although males showed significant consistency in their exploratory and mating behaviour over time (1 week), we found no evidence that these traits constituted a behavioural syndrome. Furthermore, in contrast to previous work, we found no overall effect of the light environment on any of the behaviours measured, although males responded to the treatment on an individual-level basis, as reflected by a significant individual-by-environment interaction. The future challenge is to investigate how individual consistency across different environmental contexts relates to male reproductive success.     

Recognition of foreign oviposition-marking pheromone in a multi-trophic context

Both phytophagous and parasitic insects deposit oviposition-marking pheromones (OMPs) following oviposition that function to inform conspecifics of a previously utilized host of reduced suitability. The blueberry maggot fly, Rhagoletis mendax Curran (Diptera: Tephritidae), deposits eggs individually into blueberries and then marks the fruit surface with an OMP which reduces acceptance of fruit for oviposition by conspecifics. Diachasma alloeum (Muesebeck) (Hymenoptera: Braconidae) is a parasitic wasp attacking larval R. mendax which also deposits an OMP, signaling conspecifics of a wasp-occupied host. Behavioral studies were conducted testing the hypothesis that the OMP of the parasitic wasp modifies the oviposition behavior of its host fly. In this study, we show that the OMP of D. alloeum is recognized by R. mendax, and female flies will reject wasp-marked fruit for oviposition. Thus, we present a rare demonstration of pheromonal recognition between animals occupying different taxonomic orders and trophic levels. This chemical eavesdropping may enhance the ability of the fly to avoid fruit unsuitable for larval development.     

Cover crop effects on nitrous oxide emission from a manure-treated Mollisol

Agriculture contributes 40–60% of the total annual N₂O emissions to the atmosphere. Development of management practices to reduce these emissions would have a significant impact on greenhouse gas levels. Non-leguminous cover crops are efficient scavengers of residual soil NO₃, thereby reducing leaching losses. However, the effect of a grass cover crop on N₂O emissions from soil receiving liquid swine manure has not been evaluated. This study investigated: (i) the temporal patterns of N₂O emissions following addition of swine manure slurry in a laboratory setting under fluctuating soil moisture regimes; (ii) assessed the potential of a rye (Secale cereale L.) cover crop to decrease N₂O emissions under these conditions; and (iii) quantified field N₂O emissions in response to either spring applied urea ammonium nitrate (UAN) or different rates of fall-applied liquid swine manure, in the presence or absence of a rye/oat winter cover crop. Laboratory experiments investigating cover crop effects N₂O emissions were performed in a controlled environment chamber programmed for a 14 h light period, 18 °C day temperature, and 15 °C night temperature. Treatments with or without a living rye cover crop were treated with either: (i) no manure; (ii) a phosphorus-based manure application rate (low manure): or (iii) a nitrogen-based manure application rate (high manure). We observed a significant reduction in N₂O emissions in the presence of the rye cover crop. Field experiments were performed on a fine-loamy soil in Central Iowa from October 12, 2005 to October 2, 2006. We observed no significant effect of the cover crop on cumulative N₂O emissions in the field. The primary factor influencing N₂O emission was N application rate, regardless of form or timing. The response of N₂O emission to N additions was non-linear, with progressively more N₂O emitted with increasing N application. These results indicate that while cover crops have the potential to reduce N₂O emissions, N application rate may be the overriding factor.     

European scale application of atmospheric reactive nitrogen measurements in a low-cost approach to infer dry deposition fluxes

A European scale network was established in 2006 as part of the NitroEurope Integrated Project to infer reactive nitrogen (Nr) dry deposition fluxes, based on low-cost sampling of gaseous and aerosol species and inferential modelling. The network provides monthly measurements of NH₃, NH₄⁺, HNO₃ and NO₃⁻, as well as SO₂, SO₄²⁻, HCl, Cl⁻ and base cations at 58 sites. Measurements are made with an established low-cost denuder methodology (DELTA) as a basis to: (1) examine temporal trends and spatial patterns across Europe, (2) improve and calibrate inferential modelling techniques to estimate exchange of Nr species, (3) provide best estimates of atmospheric dry N deposition, and (4) permit an analysis of net GHG exchange in relation to atmospheric and agricultural N inputs at the European scale. Responsibility for measurements is shared among seven European laboratories. An inter-comparison of the DELTA implementation by 6 laboratories at 4 test sites (Montelibretti, Italy; Braunschweig, Germany; Paterna, Spain and Auchencorth, UK) from July to October 2006 provided training for the laboratories and showed that good agreement was achieved in different climatic conditions (87% of laboratory site-means within 20% of the inter-laboratory median). Results obtained from the first year of measurements show substantial spatial variability in atmospheric Nr concentrations, illustrating the major local (NH₃) and regional (HNO₃, NO₃⁻, and NH₄⁺) differences in Nr concentrations. These results provide the basis to develop future estimates of site-based Nr dry deposition fluxes across Europe, and highlight the role of NH₃, largely of agricultural origin, which was the largest single constituent and will dominate dry Nr fluxes at most sites.     

Litter decomposition and nitrogen release in a sloping Mediterranean subtropical agroecosystem on the coast of Granada (SE, Spain): Effects of floristic and topographic alteration on the slope

On the coast of Granada (SE, Spain), an economically important area for subtropical fruit cultivation, the crops are grown on orchard terraces. Also, high amounts of fertilizers, often excessive, are used in this type of intensive agriculture. However, each year significant fractions of nutrients taken up by the trees return to the soil by fallen leaves. Using a litter-bag technique, we assessed the decomposition rates and N-release in various types of litter. Our main purpose was to compare two different agroecosystem scenarios: (1) an unaltered slope consisting mainly of a mixture of herbaceous plants (Papaver rhoeas, Convolvulus sp., Malva sylvestris, Reseda phyteuma, Anacyclus sp., Sinapis arvensis, Medicago sp.) among spontaneous perennial woody shrubs (Genista umbellata, Olea europaea, Lavandula officinalis, Phlomis purpurea, Retama sphaerocarpa), and (2) an altered slope cultivated with subtropical trees on terraces: loquat (Eriobotrya japonica), mango (Mangifera indica), avocado (Persea americana), and cherimoya (Annona cherimola), with groundcover plantings of aromatic, medicinal, and melliferous plants (AMMPs) on the taluses of the terraces, which are usually used for erosion control: Lavandula dentata, Thymus mastichina, Satureja obovata, Rosmarinus officinalis, Anthyllis cytisoides. In the leaves from the subtropical crops, we found the highest decomposition rates in cherimoya and the lowest in mango (1.30 and 0.64 years⁻¹, respectively). Leaves from mango and loquat registered initial peaks of N immobilization and later N-release, which was highest in cherimoya and avocado leaves (71.2 and 56.8% of the initial remaining N). In the spontaneous woody shrubs, O. europaea and G. umbellata were the slowest in decomposing (1.18 and 1.01 years⁻¹, respectively) contrary to L. officinalis, which decomposed fastest (2.22 years⁻¹). Only L. officinalis and P. purpurea registered a net N-release at the end of the study. The AMMPs showed different decomposition patterns: L. dentata registered the highest decomposition rates and Rosmarinus the lowest (1.9 and 1.1 years⁻¹, respectively). T. mastichina, L. dentata, and S. obovata had the highest N-release, whereas R. officinalis and A. cytisoides showed N immobilization (183 and 122% of the initial N). Knowledge of the dynamics of nutrient release and litter decomposition will be useful for predicting nutrient availability and nutrient cycles in these types of agroecosystems where subtropical orchards are grown on terraces.