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.     

Nutritional benefits of filial cannibalism in three-spined sticklebacks (<Emphasis Type="Italic">Gasterosteus aculeatus</Emphasis>)

Although filial cannibalism (eating one’s own offspring) occurs in numerous species, including several teleost fishes, its adaptive value is still not well understood. One often-discussed explanation is that individuals enhance their mass and body condition by consuming part of their eggs. However, evidence for this assumption is scarce thus far. In this study, male three-spined sticklebacks (Gasterosteus aculeatus), a species with paternal care, were allowed to care for a batch of eggs or for an empty nest under food-deprived conditions. All brood-caring males cannibalised at least part of their eggs and thus preserved their initial mass and body condition. Furthermore, mass as well as body condition was significant positively correlated with the number of cannibalised eggs. In contrast, empty-nest males that had no possibility to cannibalise eggs significantly lost mass and body condition. This is, to our knowledge, the first experimentally documented evidence that mass as well as body condition were preserved by filial cannibalism.     

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.     

A lake classification concept for a more accurate global estimate of the dissolved inorganic carbon export from terrestrial ecosystems to inland waters

The magnitude of lateral dissolved inorganic carbon (DIC) export from terrestrial ecosystems to inland waters strongly influences the estimate of the global terrestrial carbon dioxide (CO₂) sink. At present, no reliable number of this export is available, and the few studies estimating the lateral DIC export assume that all lakes on Earth function similarly. However, lakes can function along a continuum from passive carbon transporters (passive open channels) to highly active carbon transformers with efficient in-lake CO₂ production and loss. We developed and applied a conceptual model to demonstrate how the assumed function of lakes in carbon cycling can affect calculations of the global lateral DIC export from terrestrial ecosystems to inland waters. Using global data on in-lake CO₂ production by mineralization as well as CO₂ loss by emission, primary production, and carbonate precipitation in lakes, we estimated that the global lateral DIC export can lie within the range of \( {0.70}_{-0.31}^{+0.27} \) to \( {1.52}_{-0.90}^{+1.09} \) Pg C yr^?1 depending on the assumed function of lakes. Thus, the considered lake function has a large effect on the calculated lateral DIC export from terrestrial ecosystems to inland waters. We conclude that more robust estimates of CO₂ sinks and sources will require the classification of lakes into their predominant function. This functional lake classification concept becomes particularly important for the estimation of future CO₂ sinks and sources, since in-lake carbon transformation is predicted to be altered with climate change.     

Millennium-old farm breeding of Chinese softshell turtles (<Emphasis Type="Italic">Pelodiscus</Emphasis> spp.) results in massive erosion of biodiversity

Chinese softshell turtles (Pelodiscus spp.) are widely distributed, ranging from the Amur and Ussuri Rivers in the Russian Far East through the Korean Peninsula, Japan, and eastern, central, and southern China to southern Vietnam. In East and Southeast Asia, Chinese softshell turtles are traditionally exploited for food and have been farm-bred in China since the Spring and Autumn Period, more than 2400 years ago. Currently, the annual production of Pelodiscus amounts to 340,000 t in China alone. Using mitochondrial DNA (2428 bp) and five nuclear loci (3704 bp), we examined broad sampling of wild and farm-bred Pelodiscus to infer genetic and taxonomic differentiation. We discovered four previously unknown mitochondrial lineages, all from China. One lineage from Jiangxi is deeply divergent and sister to the mitochondrial lineage of Pelodiscus axenaria. The nuclear loci supported species status for P. axenaria and the new lineage from Jiangxi. Pelodiscus maackii and P. parviformis, both harboring distinct mitochondrial lineages, were not differentiated from P. sinensis in the studied nuclear markers. The same is true for two new mitochondrial lineages from Zhejiang, China, represented by only one individual each, and another new lineage from Anhui, Guangdong, Jiangxi and Zhejiang, China. However, Vietnamese turtles yielding a mitochondrial lineage clustering within P. sinensis were distinct in nuclear markers, suggesting that these populations could represent another unknown species with introgressed mitochondria. Its species status is also supported by the syntopic occurrence with P. sinensis in northern Vietnam and by morphology. In addition, we confirmed sympatry of P. axenaria and P. parviformis in Guangxi, China, and found evidence for sympatry of P. sinensis and the new putative species from Jiangxi, China. We also discovered evidence for hybridization in turtle farms and for the occurrence of alien lineages in the wild (Zhejiang, China), highlighting the risk of genetic pollution of native stock. In the face of the large-scale breeding of Pelodiscus, we claim that the long-term survival of distinct genetic lineages and species can only be assured when an upscale market segment for pure-bred softshell turtles is established, making the breeding of pure lineages lucrative for turtle farms. Our findings underline that the diversity of Pelodiscus is currently underestimated and threatened by anthropogenic admixture. We recommend mass screening of genetic and morphological variation of Chinese softshell turtles as a first step to understand and preserve their diversity.     

Meta-networks for the study of biogeographical traits in ecological networks: the Mexican hummingbird-plant assemblage

Recent studies on ecological networks have quantified the contribution of ecological, historical, and evolutionary factors on the structure of local communities of interacting species. However, the influence of species’ biogeographical traits, such as migratory habits or phylogeographical history, on ecological networks is poorly understood. Meta-networks, i.e., networks that cover large spatial extensions and include species not co-occurring locally, enable us to investigate mechanisms that operate at larger spatial scales such as migratory patterns or phylogeographical distributions, as well as indirect relationships among species through shared partners. Using a meta-network of hummingbird-plant interaction across Mexico, we illustrate the usefulness of this approach by investigating (1) how biogeographical and morphological factors associate with observed interactions and (2) how species-specific biogeographical characteristics associate with species’ network roles. Our results show that all studied hummingbird and plant species in the meta-network were interrelated, either directly or through shared partners. The meta-network was structured into modules, resulting from hummingbirds and plants interacting preferentially with subsets of species, which differed in biogeographical, and, to a lesser extent, morphological traits. Furthermore, migrants and hummingbirds from Nearctic, Transition, and widespread regions had a higher topological importance in the meta-network. Our study illustrates how meta-networks may contribute to our current knowledge on species’ biogeographical traits and biotic interactions, providing a perspective complementary to local-scale networks.     

A salamander’s toxic arsenal: review of skin poison diversity and function in true salamanders,genus <Emphasis Type="Italic">Salamandra</Emphasis>

Terrestrial salamanders of the genus Salamandra represent one of the most prominent groups of amphibians. They are mainly distributed across Europe but also reach Northern Africa and the Near East. Members of the six currently accepted species have long been known to be poisonous; however, work on their toxins was mostly published in German language, and therefore, many nuances of these studies have remained hidden from the majority of herpetologists and toxinologists. Several Salamandra species are called fire salamanders due to their highly contrasted, black-yellow colouration which probably serves to deter predators, although thorough evidence for aposematism in Salamandra is still lacking. Salamandra skin toxins do not only represent a potent antipredator defence but may also have antimicrobial effects. A better understanding of this dual function of Salamandra skin secretions is of utmost importance in the face of the emergence of a fungal disease causing catastrophic declines of fire salamanders in Central Europe, caused by the fungus Batrachochytrium salamandrivorans. In this review, we summarize the knowledge on Salamandra toxins, providing a list of the compounds so far isolated from their secretion and focusing on the bioactivity of the major compounds in Salamandra secretions, the steroidal alkaloids. We identify priorities for future research, including a screening of co-occurrence of steroidal alkaloids and tetrodotoxins in salamandrids, chemical characterization of already identified novel steroidal compounds, elucidation of the presence and role of peptides and proteins in the secretion, and experimental in vitro and in vivo study of the interactions between bioactive compounds in Salamandra skin secretions and cutaneous fungal and bacterial pathogens.     

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.