Polyploidy does not control all: Lineage‐specific average chromosome length constrains genome size evolution in ferns

Recent studies investigating the evolution of genome size diversity in ferns have shown that they have a distinctive genome profile compared with other land plants. Ferns are typically characterized by possessing medium‐sized genomes, although a few lineages have evolved very large genomes. Ferns are different from other vascular plant lineages as they are the only group to show evidence for a correlation between genome size and chromosome number. In this study, we aim to explore whether the evolution of fern genome sizes is not only shaped by chromosome number changes arising from polyploidy but also by constraints on the average amount of DNA per chromosome. We selected the genus Asplenium L. as a model genus to study the question because of the unique combination of a highly conserved base chromosome number and a high frequency of polyploidy. New genome size data for Asplenium taxa were combined with existing data and analyzed within a phylogenetic framework. Genome size varied substantially between diploid species, resulting in overlapping genome sizes among diploid and tetraploid spleenworts. The observed additive pattern indicates the absence of genome downsizing following polyploidy. The genome size of diploids varied non‐randomly and we found evidence for clade‐specific trends towards larger or smaller genomes. The 578‐fold range of fern genome sizes have arisen not only from repeated cycles of polyploidy but also through clade‐specific constraints governing accumulation and/or elimination of DNA.     

Abstracts from the 3rd Annual A-CURE Symposium

Background

Patients after aortic coarctation (CoA) repair show impaired aortic bioelasticity and altered left ventricular (LV) mechanics, predisposing diastolic dysfunction. Our purpose was to assess aortic bioelasticity and LV properties in CoA patients who underwent endovascular stenting or surgery using cardiovascular magnetic resonance (CMR) imaging.

Methods

Fifty CoA patients (20.5 ± 9.5 years) were examined by 3-Tesla CMR. Eighteen patients had previous stent implantation and 32 had surgical repair. We performed volumetric analysis of both ventricles (LV, RV) and left atrium (LA) to measure biventricular volumes, ejection fractions, left atrial (LA) volumes, and functional parameters (LAEF_Passive, LAEF_Contractile, LAEF_Reservoir). Aortic distensibility and pulse wave velocity (PWV) were assessed. Native T1 mapping was applied to examine LV tissue properties. In twelve patients post-contrast T1 mapping was performed.

Results

LV, RV and LA parameters did not differ between the surgical and stent group. There was also no significant difference for aortic distensibility, PWV and T1 relaxation times. Aortic root distensibility correlated negatively with age, BMI, BSA and weight (p < 0.001). Native T1 values correlated negatively with age, weight, BSA and BMI (p < 0.001). Lower post-contrast T1 values were associated with lower aortic arch distensibility and higher aortic arch PWV (p < 0.001).

Conclusions

CoA patients after surgery or stent implantation did not show significant difference of aortic elasticity. Thus, presumably other factors like intrinsic aortic abnormalities might have a greater impact on aortic elasticity than the approach of repair. Interestingly, our data suggest that native T1 values are influenced by demographic characteristics.

     

Quantifying and Understanding Voltage Losses Due to Nonradiative Recombination in Bulk Heterojunction Organic Solar Cells with Low Energetic Offsets

Open‐circuit voltage (V_OC) losses in organic photovoltaics (OPVs) inhibit devices from reaching V_OC values comparable to the bandgap of the donor–acceptor blend. Specifically, nonradiative recombination losses (?V_nr) are much greater in OPVs than in silicon or perovskite solar cells, yet the origins of this are not fully understood. To understand what makes a system have high or low loss, an investigation of the nonradiative recombination losses in a total of nine blend systems is carried out. An apparent relationship is observed between the relative domain purity of six blends and the degree of nonradiative recombination loss, where films exhibiting relatively less pure domains show lower ?V_nr than films with higher domain purity. Additionally, it is shown that when paired with a fullerene acceptor, polymer donors which have bulky backbone units to inhibit close π–π stacking exhibit lower nonradiative recombination losses than in blends where the polymer can pack more closely. This work reports a strategy that ensures ?V_nr can be measured accurately and reports key observations on the relationship between ?V_nr and properties of the donor/acceptor interface.     

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties

Negativicutes are gram-negative bacteria characterized by two cell membranes, but they are phylogenetically a side-branch of gram-positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from gram-negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co-evolved vertically with their hosts and thus resemble gram-positive Firmicute prophages. We predicted and characterized 485 prophages (mostly Caudovirales) from gram-negative Firmicute genomes plus 2977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to support our predictions. The majority of identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu-like candidate prophage and no clear P2-like prophages were identified in Negativicutes, both common in Proteobacteria. Given this collective evidence, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence-related prophages, which occasionally harboured antibiotic resistance genes, were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales), possibly suggesting horizontal cross-order phage infection between human gut commensals. Our results reveal ancient genomic signatures of phage and bacteria co-evolution despite horizontal phage mobilization.     

Tree species identity determines wood decomposition via microclimatic effects

Empirical evidence suggests that the rich set of ecosystem functions and nature's contributions to people provided by forests depends on tree diversity. Biodiversity–ecosystem functioning research revealed that not only species richness per se but also other facets of tree diversity, such as tree identity, have to be considered to understand the underlying mechanisms. One important ecosystem function in forests is the decomposition of deadwood that plays a vital role in carbon and nutrient cycling and is assumed to be determined by above‐ and belowground interactions. However, the actual influence of tree diversity on wood decay in forests remains inconclusive. Recent studies suggest an important role of microclimate and advocate a systematical consideration of small‐scale environmental conditions. We studied the influence of tree species richness, tree species identity, and microclimatic conditions on wood decomposition in a 12‐year‐old tree diversity experiment in Germany, containing six native species within a tree species richness gradient. We assessed wood mass loss, soil microbial properties, and soil surface temperature in high temporal resolution. Our study shows a significant influence of tree species identity on all three variables. The presence of Scots pine strongly increased wood mass loss, while the presence of Norway spruce decreased it. This could be attributed to structural differences in the litter layer that were modifying the capability of plots to hold the soil surface temperature at night, consequently leading to enhanced decomposition rates in plots with higher nighttime surface temperatures. Therefore, our study confirmed the critical role of microclimate for wood decomposition in forests and showed that soil microbial properties alone were not sufficient to predict wood decay. We conclude that tree diversity effects on ecosystem functions may include different biodiversity facets, such as tree identity, tree traits, and functional and structural diversity, in influencing the abiotic and biotic soil properties.     

Application of a SSR‐GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics

By applying second‐generation sequencing technologies to microsatellite genotyping, sequence information is produced which can result in high‐resolution population genetics analysis populations and increased replicability between runs and laboratories. In the present study, we establish an approach to study the genetic structure patterns of two European hedgehog species Erinaceaus europaeus and E. roumanicus. These species are usually associated with human settlements and are good models to study anthropogenic impacts on the genetic diversity of wild populations. The short sequence repeats genotyping by sequence (SSR‐GBS) method presented uses amplicon sequences to determine genotypes for which allelic variants can be defined according to both length and single nucleotide polymorphisms (SNPs). To evaluate whether complete sequence information improved genetic structure definition, we compared this information with datasets based solely on length information. We identified a total of 42 markers which were successfully amplified in both species. Overall, genotyping based on complete sequence information resulted in a higher number of alleles, as well as greater genetic diversity and differentiation between species. Additionally, the structure patterns were slightly clearer with a division between both species and some potential hybrids. There was some degree of genetic structure within species, although only in E. roumanicus was this related to geographical distance. The statistically significant results obtained by SSR‐GBS demonstrate that it is superior to electrophoresis‐based methods for SSR genotyping. Moreover, the greater reproducibility and throughput with lower effort which can be obtained with SSR‐GBS and the possibility to include degraded DNA into the analysis, allow for continued relevance of SSR markers during the genomic era.     

Early emergence increases survival of tree seedlings in Central European temperate forests despite severe late frost

Global warming is expected to result in earlier emergence of tree seedlings that may experience higher damages and mortality due to late frost in spring. We monitored emergence, characteristics, and survival of seedlings across ten tree species in temperate mixed deciduous forests of Central Europe over one and a half year. We tested whether the timing of emergence represents a trade‐off for seedling survival between minimizing frost risk and maximizing the length of the growing period. Almost two‐thirds of the seedlings died during the first growing period. The timing of emergence was decisive for seedling survival. Although seedlings that emerged early faced a severe late frost event, they benefited from a longer growing period resulting in increased overall survival. Larger seedling height and higher number of leaves positively influenced survival. Seedlings growing on moss had higher survival compared to mineral soil, litter, or herbaceous vegetation. Synthesis. Our findings demonstrate the importance of emergence time for survival of tree seedlings, with early‐emerging seedlings more likely surviving the first growing period.     

A mutation of keratin 18 within the coil 1A consensus motif causes widespread keratin aggregation but cell type-restricted lethality in mice

Mutations in genes encoding epidermal keratins cause skin disorders, while those in internal epithelial keratins, such as K8 and K18, are risk factors for liver diseases. The effect of dominant mutations in K8 or K18 during embryonic development and tissue homeostasis has not been examined so far. Here we demonstrate that the dominant mutation hK18 R89C, that is highly similar to hK14 R125C, causing EBS in humans, leads to cell type-specific lethality in mice, depending on the ratio of mutant to endogenous keratins. Mice expressing hK18 R89C in the absence of endogenous K19 and K18 died at mid-gestation from defects in trophoblast giant cells, accompanied by haematomas. A single, endogenous K18 allele rescued embryonic lethality but caused aggregation of keratins in all adult internal epithelia, surprisingly without spontaneous cell fragility. Closer analysis revealed that both filaments and aggregates coexisted in the same cell, depending on the ratio of mutant to endogenous keratins. Our results demonstrate that balanced overexpression of a wild-type keratin rescued the lethal consequences of a dominant-negative mutation. This has important implications for therapy approaches of keratinopathies, suggesting that suppressing the mutant allele is not necessary in vivo.     

Genome wide association (GWA) study for early onset extreme obesity supports the role of fat mass and obesity associated gene (FTO) variants

Background

Obesity is a major health problem. Although heritability is substantial, genetic mechanisms predisposing to obesity are not very well understood. We have performed a genome wide association study (GWA) for early onset (extreme) obesity.

Methodology/Principal Findings

a) GWA (Genome-Wide Human SNP Array 5.0 comprising 440,794 single nucleotide polymorphisms) for early onset extreme obesity based on 487 extremely obese young German individuals and 442 healthy lean German controls; b) confirmatory analyses on 644 independent families with at least one obese offspring and both parents. We aimed to identify and subsequently confirm the 15 SNPs (minor allele frequency ≥10%) with the lowest p-values of the GWA by four genetic models: additive, recessive, dominant and allelic. Six single nucleotide polymorphisms (SNPs) in FTO (fat mass and obesity associated gene) within one linkage disequilibrium (LD) block including the GWA SNP rendering the lowest p-value (rs1121980; log-additive model: nominal p = 1.13×10⁻⁷, corrected p = 0.0494; odds ratio (OR)_CT 1.67, 95% confidence interval (CI) 1.22–2.27; OR_TT 2.76, 95% CI 1.88–4.03) belonged to the 15 SNPs showing the strongest evidence for association with obesity. For confirmation we genotyped 11 of these in the 644 independent families (of the six FTO SNPs we chose only two representing the LD bock). For both FTO SNPs the initial association was confirmed (both Bonferroni corrected p<0.01). However, none of the nine non-FTO SNPs revealed significant transmission disequilibrium.

Conclusions/Significance

Our GWA for extreme early onset obesity substantiates that variation in FTO strongly contributes to early onset obesity. This is a further proof of concept for GWA to detect genes relevant for highly complex phenotypes. We concurrently show that nine additional SNPs with initially low p-values in the GWA were not confirmed in our family study, thus suggesting that of the best 15 SNPs in the GWA only the FTO SNPs represent true positive findings.