All-in-one whole exome sequencing strategy with simultaneous copy number variant,single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience

Objective

We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result.

Methods

After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis.

Results

In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days.

Conclusion

We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.     

How do nutrient conditions and species identity influence the impact of mesograzers in eelgrass-epiphyte systems?

Coastal eutrophication is thought to cause excessive growth of epiphytes in eelgrass beds, threatening the health and survival of these ecologically and economically valuable ecosystems worldwide. Mesograzers, small crustacean and gastropod grazers, have the potential to prevent seagrass loss by grazing preferentially and efficiently on epiphytes. We tested the impact of three mesograzers on epiphyte biomass and eelgrass productivity under threefold enriched nutrient concentrations in experimental indoor mesocosm systems under summer conditions. We compared the results with earlier identical experiments that were performed under ambient nutrient supply. The isopod Idotea baltica, the periwinkle Littorina littorea, and the small gastropod Rissoa membranacea significantly reduced epiphyte load under high nutrient supply with Rissoa being the most efficient grazer, but only high densities of Littorina and Rissoa had a significant positive effect on eelgrass productivity. Although all mesograzers increased epiphyte ingestion with higher nutrient load, most likely as a functional response to the quantitatively and qualitatively better food supply, the promotion of eelgrass growth by Idotea and Rissoa was diminished compared to the study performed under ambient nutrient supply. Littorina maintained the level of its positive impact on eelgrass productivity regardless of nutrient concentrations.     

Mushroom harvesting ants in the tropical rain forest

Ants belong to the most important groups of arthropods, inhabiting and commonly dominating most terrestrial habitats, especially tropical rainforests. Their highly collective behavior enables exploitation of various resources and is viewed as a key factor for their evolutionary success. Accordingly, a great variety of life strategies evolved in this group of arthropods, including seed harvesters, gardeners, and planters, fungus growers, nomadic hunters, life stock keepers, and slave makers. This study reports the discovery of a new lifestyle in ants. In a Southeast Asian rainforest habitat, Euprenolepis procera is specialized in harvesting a broad spectrum of naturally growing mushrooms, a nutritionally challenging and spatiotemporally unpredictable food source. While unfavorable to the vast majority of animals, E. procera has developed exceptional adaptations such as a shift to a fully nomadic lifestyle and special food processing capabilities, which allow it to rely entirely on mushrooms. As a consequence, E. procera is the most efficient and predominant consumer of epigeic mushrooms in the studied habitat and this has broad implications for the tropical rainforest ecosystem.     

Regional,seasonal and interspecific variation in <Superscript>15</Superscript>N and <Superscript>13</Superscript>C in sympatric mouse lemurs

Madagascar provides some of the rare examples where two or more primate species of the same genus and with seemingly identical niche requirements occur in sympatry. If congeneric primate species co-occur in other parts of the world, they differ in size in a way that is consistent with Hutchinson’s rule for coexisting species, or they occupy different ecological niches. In some areas of Madagascar, mouse lemurs do not follow these “rules” and thus seem to violate one of the principles of community ecology. In order to understand the mechanisms that allow coexistence of sympatric congeneric species without obvious niche differentiation, we studied food composition of two identical sized omnivorous mouse lemur species, Microcebus griseorufus and M. murinus with the help of stable isotope analyses (δ ¹⁵N and δ ¹³C). The two species are closely related sister species. During the rich season, when food seems abundant, the two species do not differ in their nitrogen isotope composition, indicating that the two species occupy the same trophic level. But they differ in their δ ¹³C values, indicating that M. griseorufus feeds more on C₄ and CAM (Crassulacean-acid-metabolism) plants than M. murinus. During the lean season, M. murinus has lower δ ¹⁵N values, indicating that the two species feed at different trophic levels during times of food shortage. Hybrids between the two species showed intermediate food composition. The results reflect subtle differences in foraging or metabolic adaptations that are difficult to quantify by traditional observations but that represent possibilities to allow coexistence of species.     

An economic assessment of drought effects on three grassland systems in Switzerland

This paper analyzes the economic impacts of summer drought on Swiss grassland production. We combine field trial data from drought experiments in three different grasslands in Switzerland with site-specific information on economic costs and benefits. The analysis focuses on the economic implications of drought effects on grassland yields as well as grassland composition. In agreement with earlier studies, we found rather heterogeneous yield effects of drought on Swiss grassland systems, with significantly reduced yields as a response to drought at the lowland and sub-alpine sites, but increased yields at the wetter pre-alpine site. Relative yield losses were highest at the sub-alpine site (with annual yield losses of up to 37 %). However, because income from grassland production at extensive sites relies to a large extent on ecological direct payments, even large yield losses had only limited implications in terms of relative profit reductions. In contrast, negative drought impacts at the most productive, intensively managed lowland site were dominant, with average annual drought-induced profit margin reductions of about 28 %. This is furthermore emphasized if analyzing the farm level perspective of drought impacts. Combining site-specific effects at the farm level, we found that in particular farms with high shares of lowland grassland sites suffer from summer droughts in terms of farm-level fodder production and profit margins. Moreover, our results showed that the higher competitiveness of weeds (broad-leaved dock) under drought conditions will require increasing attention on weed control measures in future grassland production systems. Taking into account that the risk of drought occurrence is expected to increase in the coming years, additional instruments to cope with drought risks in fodder production and finally farmers’ income have to be developed.     

A Force for Renewal in Academia

I start my essay by recalling the resistance at my university towards some groundbreaking results from environmental and global food production research in the early 1960s, when I was a student in agricultural sciences. I describe this resistance as academic inertia originating from group think in the scientific community. I argue that the problems we face today in our search for sustainable development on a global level require a long-term and broad systems approach in research. I conclude that the predominant scientific paradigm, which I define as the control paradigm, is insufficient given its inbuilt reductionist bias. We need the complement of a paradigm entailing a holistic perspective, which I call the co-existence paradigm. I explore how academic inertia and an increasingly competitive culture in the academic world counteract this development. Students at Uppsala University have managed to cross the boundaries of academic inertia in this area by establishing a Center for Environment and Development Studies which pursues a holistic and multidisciplinary perspective. The student-run center, called Cemus, has successfully acted as a force for renewal in academia for two decades. I describe how the center works and suggest that Cemus represents a model for institutionalizing renewal in academia that fills an essential function and is applicable for any university in a democratic society.