Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches

Objectives

To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches.

Methods

Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses.

Results

The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus.

Conclusions

ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.     

Understanding conservation conflicts associated with rodent outbreaks in farmland areas

Rodent outbreaks affect many farmland areas worldwide and the negative environmental impacts of control campaigns cause intense social tensions. In such conservation conflicts, understanding stakeholders’ viewpoints is critical to promote ecologically sustainable management. We used Q-methodology, a framework standing between qualitative and quantitative social research, to investigate human subjectivity and understand conflicts caused by rodent outbreaks in Spain. We interviewed farmers, conservationists, hunters, and governmental agencies, and identified five main discourses about the origins and consequences of the conflictive situation. Finding sustainable management is impaired by opposing views about causes and consequences of vole outbreaks and their management, which are at the root of the conflict. Social tensions will likely remain until the underlying conflicts between people holding different views are also managed. Decision-making should therefore focus on mitigating underlying conflicts. Using trained independent mediators would help the effective resolution of conservation conflicts caused by rodent outbreaks and their management.

     

Temporal changes in the trophic ecology of the asymbiotic gorgonian Leptogorgia virgulata

Gorgonians are widespread sub-littoral benthic suspension feeders in the world oceans. However, data on their trophic ecology and role in benthic–pelagic coupling and biogeochemical cycles remain limited. This study assesses the trophic ecology of Leptogorgia virgulata in the Skidaway River estuary, USA (31.9896N, 81.0242W) by analysing carbon and nitrogen isotopic signatures of its soft tissue and different-sized fractions of particulate organic matter (POM) in its environment. Samples were taken in 5 April, 2 August, and 15 October 2012 and 11 January 2013. Results support a distinct temporal shift in the diet of L. virgulata from the POM fraction <10 µm (i.e. pico- and nanoplankton) to the 10–63-µm fraction (i.e. microplankton). This trophic regime is likely associated with the natural abundance of prey items within these size classes, thus suggesting that L. virgulata may be an opportunistic feeder, and seasonal shifts in food availability in the water column affect its diet. As such small prey items affect the bioenergetics of L. virgulata, it is important to understand the implications of changes in food availability associated with environmental drivers on the physiology and population dynamics of this dominant species in the western Atlantic Ocean.     

Macrofaunal responses to structural complexity are mediated by environmental variability and surrounding habitats

Investigating the context that surrounds each habitat is crucial to understand local responses of assemblages of species to habitats. Here, I tested whether responses of benthic macroinvertebrates to the structural complexity of experimental habitats were mediated by the characteristics of their surrounding habitats (i.e. rockpools or emergent-rock surfaces). Each type of surrounding habitat provided particular biotic (e.g. algal growth) and abiotic (e.g. temperature, water movement) conditions that were expected to affect benthic assemblages. The results show that (1) composition of entire assemblages was affected by the matrix and type of habitat; (2) effects of the matrix on the number of species varied depending on the different types of habitats; (3) abundant species showed specific responses to type of habitat, independently of the matrix; and (4) relationships between numbers of species and two major environmental variables (i.e. micro-algal biomass and sediment) varied depending on the type of habitats and the surrounding matrix. Generally, these findings demonstrate that understanding the consequences of the spatial structure of these habitats is essential to advance our knowledge on patterns of abundance and distributions of functionally important species and ultimately the structure of intertidal assemblages.     

Variable within-brood maternal provisioning in newly extruded embryos of Homarus gammarus

Offspring quality of decapod crustaceans has been widely studied, with special emphasis on the sources of variability determining embryonic and larval quality. Nevertheless, maternal provisioning has commonly been overlooked as a potential source of offspring within-brood variability. In the present study, the existence of variable maternal provisioning was assessed through the analysis of the fatty acid (FA) profile of newly extruded embryos from different regions of the brooding chamber of Homarus gammarus. Significant differences in the FA profile of embryos sampled from different pleopods and sides of the brooding chamber were recorded. Significant deviations of the overall mean of each surveyed female were also observed for essential FA, particularly 20:4n-6, 20:5n-3 and 22:6n-3. Lipid energy available to fuel embryogenesis also varied among embryos sampled from different regions of the brooding chamber. Results suggest variable female investment at oocyte production, which may be amplified during the incubation period of developing embryos by differential lipid catabolism. For the first time, maternal provisioning is evidenced as an additional source for within-brood variability in the FA profile of embryos.     

Life history strategy of a southern European population of brown shrimp (Crangon crangon L.): evidence for latitudinal changes in growth phenology and population dynamics

This study provides a comprehensive examination of the life cycle dynamics of the brown shrimp (Crangon crangon L.) in the Mondego estuary, Portugal, a habitat located near the southern edge of the range of this species in European waters. The phenology of all life stages was documented (from the occurrence of ovigerous females, developing embryos, planktonic larvae and benthic post-larvae), and migration patterns of larvae into and out of the estuary were examined. Temperature-dependent functions of egg and larval development were combined with data on field abundance to predict the timing and magnitude of occurrence of larvae and recruits. Compared to brown shrimp at higher latitudes, southern conspecifics grow slower, mature earlier and have smaller brood sizes, and larvae have a more protracted settlement period. The Mondego estuary, besides acting as nursery area, is a dynamic platform for C. crangon to use in different stages, sizes and seasons.     

An indexed dispersion criterion for testing the sex-biased dispersal of lek mating behavior of capercaillies

Traditionally it has been assumed by ecologists that the dispersion of positions with respect to leks of female capercaillies during the mating season is superior to the dispersion of positions of male capercaillies. However some recently published articles suggest the idea that dispersion is not sex-biased, but both sexes show a similar dispersion. This article introduces a mathematical model to approach the study of the above question by means of an indexed dispersion criterion. This model is developed in detail thus deriving its main mathematical properties. On this basis, the model is applied to the analysis of the motivating problem with real data of positions of leks and female and male capercaillies. The results derived by means of the model put into doubt the traditional assumption of a superior dispersion of females supporting the new theories, that is, both sexes show a similar dispersion.