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.     

Anatomic and acoustic sexual dimorphism in the sound emission system of Phoenicoprocta capistrata (Lepidoptera: Arctiidae)

Both sexes of Phoenicoprocta capistrata have functional tymbals. The scanning electron microscopy revealed differences in the morphology of these organs in males and females. Male tymbals have a well-developed striated band, constituted by 21 ± 2 regularly arranged striae whereas female tymbals lack a striated band. This type of sexual dimorphism is rare in Arctiidae. The recording of the sound produced by moths held by the wings revealed that while males produced trains of pulses organized in modulation cycles, females produced clicks at low repetition rate following very irregular patterns. Statistically, there are differences between sexes in terms of the duration of pulses, which were 355 ± 24 μs in the case of males and 289 ± 29 μs for females. The spectral characteristics of the pulses also show sexual dimorphism. Male pulses are more tuned (Q ₁₀ = 5.2 ± 0.5) than female pulses (Q ₁₀ = 2.7 ± 0.5) and have a higher best frequency (42 ± 1 kHz vs. 29 ± 2 kHz). To our knowledge, this is the first report on an arctiid moth showing sexual dimorphism in tymbal’s anatomy that leads to a best frequency dimorphism. Males produce sound at mating attempts. The sounds recorded during mating are modulation cycles with the same spectral characteristics as those recorded when males are held by the wings. The morphological and acoustic features of female tymbals could indicate a process of degeneration and adaptation to conditions under which the emission of complex patterns is not necessary. Frank Coro no longer works at Universidad de La Habana.     

An epicuticular multilayer reflector generates the iridescent coloration in chrysidid wasps (Hymenoptera, Chrysididae)

Chrysidid wasps in the subfamily Chrysidinae are brood parasitoids or cleptoparasites of other insects and famous for their cuticular iridescence. In this study, we examine the dorsal abdominal cuticle of the chrysidid wasp Hedychrum rutilans to identify the underlying color mechanism. Using scanning electron microscopy, reflectance spectral analysis, and theoretical calculations, we demonstrate the presence of an epicuticular multilayer reflector consisting of six lamellae with a thickness of 185 nm each. The lamellae exhibit a rough surface probably functioning as spacers between the individual layers. The reflector has a measured reflectance maximum at λ = 630 nm, i.e., in the red part of the visible spectrum of light at normal incidence and the reflectance maximum shifts to green as the angle of incidence increases. Complementary theoretical modeling corroborates the view that the epicuticular multilayer generates the iridescent color of the chrysidid cuticle. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Seasonal changes in eicosanoid metabolism in the brown bear

Polyunsaturated fatty acids (PUFAs) exert several important functions across organ systems. During winter, hibernators divert PUFAs from oxidation, retaining them in their tissues and membranes, to ensure proper body functions at low body temperature. PUFAs are also precursors of eicosanoids with pro- and anti-inflammatory properties. This study investigated seasonal changes in eicosanoid metabolism of free-ranging brown bears (Ursus arctos). By using a lipidomic approach, we assessed (1) levels of specific omega-3 and omega-6 fatty acids involved in the eicosanoid cascade and (2) concentrations of eicosanoids in skeletal muscle and blood plasma of winter hibernating and summer active bears. We observed significant seasonal changes in the specific omega-3 and omega-6 precursors. We also found significant seasonal alterations of eicosanoid levels in both tissues. Concentrations of pro-inflammatory eicosanoids, such as thromboxane B2, 5-hydroxyeicosatetraenoic acid (HETE), and 15-HETE and 18-HETE, were significantly lower in muscle and/or plasma of hibernating bears compared to summer-active animals. Further, plasma and muscle levels of 5,6-epoxyeicosatrienoic acid (EET), as well as muscle concentration of 8,9-EET, tended to be lower in bears during winter hibernation vs. summer. We also found lower plasma levels of anti-inflammatory eicosanoids, such as 15dPGJ₂ and PGE₃, in bears during winter hibernation. Despite of the limited changes in omega-3 and omega-6 precursors, plasma and muscle concentrations of the products of all pathways decreased significantly, or remained unchanged, independent of their pro- or anti-inflammatory properties. These findings suggest that hibernation in bears is associated with a depressed state of the eicosanoid cascade.     

Optimisation of a PMAxx™-RT-qPCR Assay and the Preceding Extraction Method to Selectively Detect Infectious Murine Norovirus Particles in Mussels

Human noroviruses are a major cause for gastroenteritis outbreaks. Filter-feeding bivalve molluscs, which accumulate noroviruses in their digestive tissues, are a typical vector for human infection. RT-qPCR, the established method for human norovirus detection in food, does not allow discrimination between infectious and non-infectious viruses and can overestimate potentially infectious viral loads. To develop a more accurate method of infectious norovirus load estimation, we combined intercalating agent propidium monoazide (PMAxx™)-pre-treatment with RT-qPCR assay using in vitro-cultivable murine norovirus. Three primer sets targeting different genome regions and diverse amplicon sizes were used to compare one-step amplification of a short genome fragment to three two-step long-range RT-qPCRs (7 kbp, 3.6 kbp and 2.3 kbp amplicons). Following initial assays performed on untreated infectious, heat-, or ultraviolet-inactivated murine noroviruses in PBS suspension, PMAxx™ RT-qPCRs were implemented to detect murine noroviruses subsequent to their extraction from mussel digestive tissues; virus extraction via anionic polymer-coated magnetic beads was compared with the proteinase K-dependent ISO norm. The long-range RT-qPCR process detecting fragments of more than 2.3 kbp allowed accurate estimation of the infectivity of UV-damaged murine noroviruses. While proteinase K extraction limited later estimation of PMAxx™ pre-treatment effects and was found to be unsuited to the assay, magnetic bead-captured murine noroviruses retained their infectivity. Genome copies of heat-inactivated murine noroviruses differed by 2.3 log₁₀ between RT-qPCR and PMAxx™-RT-qPCR analysis in bivalve molluscs, the PMAxx™ pre-treatment allowing a closer approximation of infectious titres. The combination of bead-based virus extraction and PMAxx™ RT-qPCR thus provides a more accurate model for the estimation of noroviral bivalve mollusc contamination than the conjunction of proteinase K extraction and RT-qPCR and has the potential (once validated utilising infectious human norovirus) to provide an added measure of security to food safety authorities in the hazard assessment of potential bivalve mollusc contamination.

     

Assessment of Viral Contamination of Five Brazilian Artisanal Cheese Produced from Raw Milk: a Randomized Survey

Food and Environmental Virology - Enteric viruses have been described as important contaminants in fresh and ready-to-eat foods such as sandwiches, deli meat and dairy products. This is a...     

Ecological restoration as a strategy for mitigating and adapting to climate change: lessons and challenges from Brazil

Climate change is a global phenomenon that affects biophysical systems and human well-being. The Paris Agreement of the United Nations Framework Convention on Climate Change entered into force in 2016 with the objective of strengthening the global response to climate change by keeping global temperature rise this century well below 2 °C above pre-industrial levels and to pursue efforts to limit the temperature increase even further to 1.5 °C. The agreement requires all Parties to submit their “nationally determined contributions” (NDCs) and to strengthen these efforts in the years ahead. Reducing carbon emissions from deforestation and forest degradation is an important strategy for mitigating climate change, particularly in developing countries with large forests. Extensive tropical forest loss and degradation have increased awareness at the international level of the need to undertake large-scale ecological restoration, highlighting the need to identify cases in which restoration strategies can contribute to mitigation and adaptation. Here we consider Brazil as a case study to evaluate the benefits and challenges of implementing large-scale restoration programs in developing countries. The Brazilian NDC included the target of restoring and reforesting 12 million hectares of forests for multiple uses by 2030. Restoration of native vegetation is one of the foundations of sustainable rural development in Brazil and should consider multiple purposes, from biodiversity and ecosystem services conservation to social and economic development. However, ecological restoration still presents substantial challenges for tropical and mega-diverse countries, including the need to develop plans that are technically and financially feasible, as well as public policies and monitoring instruments that can assess effectiveness. The planning, execution, and monitoring of restoration efforts strongly depend on the context and the diagnosis of the area with respect to reference ecosystems (e.g., forests, savannas, grasslands, wetlands). In addition, poor integration of climate change policies at the national and subnational levels and with other sectorial policies constrains the large-scale implementation of restoration programs. The case of Brazil shows that slowing deforestation is possible; however, this analysis highlights the need for increased national commitment and international support for actions that require large-scale transformations of the forest sector regarding ecosystem restoration efforts. Scaling up the ambitions and actions of the Paris Agreement implies the need for a global framework that recognizes landscape restoration as a cost-effective nature-based solution and that supports countries in addressing their remaining needs, challenges, and barriers.

     

Chemical looping with oxygen uncoupling: an advanced biomass combustion technology to avoid CO2 emissions

Mitigation and Adaptation Strategies for Global Change - Bioenergy with carbon dioxide (CO2) capture and storage (BECCS) technologies represent an interesting option to reach negative carbon...