Exome sequencing for gene discovery in lethal fetal disorders – harnessing the value of extreme phenotypes

Massively parallel sequencing has revolutionized our understanding of Mendelian disorders, and many novel genes have been discovered to cause disease phenotypes when mutant. At the same time, next-generation sequencing approaches have enabled non-invasive prenatal testing of free fetal DNA in maternal blood. However, little attention has been paid to using whole exome and genome sequencing strategies for gene identification in fetal disorders that are lethal in utero, because they can appear to be sporadic and Mendelian inheritance may be missed. We present challenges and advantages of applying next-generation sequencing approaches to gene discovery in fetal malformation phenotypes and review recent successful discovery approaches. We discuss the implication and significance of recessive inheritance and cross-species phenotyping in fetal lethal conditions. Whole exome sequencing can be used in individual families with undiagnosed lethal congenital anomaly syndromes to discover causal mutations, provided that prior to data analysis, the fetal phenotype can be correlated to a particular developmental pathway in embryogenesis. Cross-species phenotyping allows providing further evidence for causality of discovered variants in genes involved in those extremely rare phenotypes and will increase our knowledge about normal and abnormal human developmental processes. Ultimately, families will benefit from the option of early prenatal diagnosis. © 2014 John Wiley & Sons, Ltd.     

Combination of two indication systems in pre-alpine lakes — diatom index and macrophyte index

Since the climax of eutrophication in the early 1980s mainly greater lakes have been investigated and monitored in terms of their nutrient charge. In the future there will still be a need to develop guidelines for monitoring the trophic status of smaller lakes. Four small lakes were investigated by the author in the years 1996 and 1997. In order to define the nutrient charge of those lakes more precisely, special emphasis has been put upon the two criteria diatoms and macrophytes. Eventually an evaluation of the lakes' catchment areas will also be an important component of these studies. Benthic diatoms are the main part of periphyton. As unicellular fast reproducing organisms they are excellent indicators for trophic situations in lakes. The diatom index denotes the trophic status of the littoral zone during the last few weeks before sampling. The macrophytes, however, reflect the nutrient charge over a longer period, i.e. several years. The macrophyte index is based on the fact that some species are most prevalent at certain nutrient loads. The effort to combine these two indication systems carries a high resolution of spatial nutrient changes as well as in temporally changes.     

SARS-CoV2 (COVID-19) infection: is fetal surgery in times of national disasters reasonable?

Even though the global COVID-19 pandemic may affect how medical care is delivered in general, most countries try to maintain steady access for women to routine pregnancy care, including fetal anomaly screening. This means that, also during this pandemic, fetal anomalies will be detected, and that discussions regarding invasive genetic testing and possibly fetal therapy will need to take place. For patients, concerns about Severe Acute Respiratory Syndrome-Corona Virus 2 will add to the anxiety caused by the diagnosis of a serious fetal anomaly. Yet, also for fetal medicine teams the situation gets more complex as they must weigh up the risks and benefits to the fetus as well as the mother, while managing a changing evidence base and logistic challenges in their healthcare system.     

Genotypic variation in the parasitic dinoflagellate Hematodinium perezi along the Delmarva Peninsula,Virginia

Hematodinium perezi (genotype III) is a parasitic dinoflagellate that infects blue crabs along the eastern seaboard and Gulf of Mexico, USA. In order to examine the intra-specific genetic variation of this parasite, eleven microsatellite markers from H. perezi (III) were amplified from 227 infected blue crabs collected during 2008–2009 from six sites in Virginia. Simultaneous infections with multiple genetic types in a single-host individual were common and observed in 42 % of the samples. The remaining 58 % of samples had a single allele per locus at all eight polymorphic loci suggesting that the life history stages of the parasite in the host hemolymph are likely haploid. The composition and distribution of multi-locus genotypes (MLG) from samples with infections of a single genetic type indicated high genotypic variation along the Delmarva Peninsula, Virginia, with no evidence of population structure. The lack of linkage disequilibrium combined with the large number of unique MLGs (84 %) is strong evidence for recombination in the life cycle, but the sexual stages remain undetermined. This is the first evidence of ploidy level, infections by multiple genetic types in an individual host animal, high levels of genotypic variation, and sexual reproduction for any species of Hematodinium.     

What are the strengths and limitations of direct and indirect assessment of dispersal? Insights from a long-term field study in a group-living bird species

Molecular methods of assessing dispersal have become increasingly powerful and have superseded direct methods of studying dispersal. Although now less popular, direct methods of studying dispersal remain important tools for understanding the evolution of dispersal. Here, we use data from Siberian jays Perisoreus infaustus, a group-living bird species, to compare natal dispersal distances and rates using visual mark–recapture, radio-tracking and microsatellite data. Siberian jays have bimodal natal dispersal timing; socially dominant offspring remain with their parents for up to 5 years (delayed dispersers), while they force their subordinate brood mates to leave the parental territory at independence (early dispersers). Early dispersers moved about 9,000 m (visual mark–recapture, radio-tracking) before settling in a group as a non-breeder. In contrast, delayed dispersers moved about 1,250 m (visual mark–recapture only) and mainly moved to a breeding opening. Dispersal distances were greater in managed habitat compared to natural habitat for both early and delayed dispersers. Molecular estimates based on 23 microsatellite loci and geographical locations supported distance estimates from the direct methods. Our study shows that molecular methods are at least 22 times cheaper than direct methods and match estimates of dispersal distance from direct methods. However, molecular estimates do not give insight into the behavioural mechanisms behind dispersal decisions. Thus, to understand the evolution of dispersal, it is important to combine direct and indirect methods, which will give insights into the behavioural processes affecting dispersal decisions, allowing proximate dispersal decisions to be linked to the ultimate consequences thereof.     

Testing a post-copulatory pre-zygotic reproductive barrier in a passerine species pair

Sexual selection may drive speciation, but most research focuses on pre-copulatory sexual selection, overlooking post-copulatory processes. Post-copulatory sexual selection in allopatric populations could drive divergence in post-copulatory pre-zygotic (PCPZ) phenotypes, limiting gene flow upon secondary contact. Here, we performed in vitro experiments examining one potential PCPZ barrier between two closely related passerine species, house sparrows (Passer domesticus) and Spanish sparrows (Passer hispaniolensis). In birds, crossing in the vagina may be particularly challenging for sperm, so we tested the effect of female reproductive tract fluids on sperm swimming speed and motility. If a PCPZ barrier exists at this stage of the fertilization process, heterospecific female fluids are predicted to reduce sperm swimming speed or motility relative to conspecific female fluid. We found that house sparrow female fluids affected the two species’ sperm asymmetrically, depending on the control sperm velocity and male species. Overall, however, sperm performed equally in conspecific and heterospecific female fluids, and the species had similar sperm morphology and sperm swimming performance. Low divergence in PCPZ phenotypes between species, perhaps because post-copulatory sexual selection is stabilizing or only moderately strong in these taxa, may be insufficient to cause an overall PCPZ barrier. Reinforcement may be unlikely to drive PCPZ barriers for this species pair, because relatively effective pre-copulatory barriers exist between the species, and because hybrids can be quite successful. Testing the role of PCPZ barriers in birds with more divergent PCPZ phenotypes will improve our understanding of speciation in passerines.