Evaluation of polygenic prediction methodology within a reference-standardized framework

The predictive utility of polygenic scores is increasing, and many polygenic scoring methods are available, but it is unclear which method performs best. This study evaluates the predictive utility of polygenic scoring methods within a reference-standardized framework, which uses a common set of variants and reference-based estimates of linkage disequilibrium and allele frequencies to construct scores. Eight polygenic score methods were tested: p-value thresholding and clumping (pT+clump), SBLUP, lassosum, LDpred1, LDpred2, PRScs, DBSLMM and SBayesR, evaluating their performance to predict outcomes in UK Biobank and the Twins Early Development Study (TEDS). Strategies to identify optimal p-value thresholds and shrinkage parameters were compared, including 10-fold cross validation, pseudovalidation and infinitesimal models (with no validation sample), and multi-polygenic score elastic net models. LDpred2, lassosum and PRScs performed strongly using 10-fold cross-validation to identify the most predictive p-value threshold or shrinkage parameter, giving a relative improvement of 16–18% over pT+clump in the correlation between observed and predicted outcome values. Using pseudovalidation, the best methods were PRScs, DBSLMM and SBayesR. PRScs pseudovalidation was only 3% worse than the best polygenic score identified by 10-fold cross validation. Elastic net models containing polygenic scores based on a range of parameters consistently improved prediction over any single polygenic score. Within a reference-standardized framework, the best polygenic prediction was achieved using LDpred2, lassosum and PRScs, modeling multiple polygenic scores derived using multiple parameters. This study will help researchers performing polygenic score studies to select the most powerful and predictive analysis methods.     

Progressive atrophy of the thymus in mice carrying Lewis lung carcinoma grafts

Summary A rapid and progressive thymus atrophy in B₆D₂ mice following transplantation of Lewis lung carcinoma cells is reported. Spleen weight, however, increased in tumor-carrying animals. Tumor extracts failed to induce these alterations. The mechanism of these perturbations of the immune system in tumor-carrying animals is discussed.This work was supported by the Norwegian Cancer Society     

Why the free floating macrophyte Stratiotes aloides mainly grows in highly CO2-supersaturated waters

We examined how the freely floating macrophyte, Stratiotes aloides L., sampled from a CO₂-supersaturated pond, changes leaf morphology, photosynthesis and inorganic carbon acquisition during its different submerged and emerged life stages in order to evaluate whether S. aloides requires consistently supersaturated CO₂ conditions to grow and complete its life cycle. Submerged rosettes formed from over-wintering turions had typical traits of submerged plants with high specific leaf area and low chlorophyll a concentrations. Emergent leaf parts of mature, floating specimens had typical terrestrial traits with stomata, low specific leaf area and high chlorophyll a content, while offsets formed vegetatively and basal, submerged parts of mature plants showed traits in between. All submerged leaf types exhibited some ability to use HCO₃⁻ but only rosettes formed from turions had efficient HCO₃⁻ use. Rosettes also had the highest CO₂ affinity and maximum CO₂-saturated photosynthesis in water. Half-saturation constants for CO₂ (21–74 μM CO₂) were for all submerged leaf parts 5–140 times lower than the concentrations of free CO₂ in the pond (350–2800 μM CO₂). Emergent leaves were less efficient in water but had significantly higher photosynthesis than submerged, mature leaf parts in air, and rates of photosynthesis of emergent leaves in air were three to five times higher than rates of CO₂-saturated photosynthesis of the three submerged leaf types in water. Underwater photosynthetic rates estimated at CO₂ concentrations corresponding to air equilibrium were not sufficiently high to support any noticeable growth except for rosettes, in which bicarbonate utilization combined with high CO₂ affinity resulted in photosynthetic rates corresponding to almost 34% of maximum rates at high free CO₂. We conclude that S. aloides requires consistently high CO₂-supersaturation to support high growth and to complete its life cycle, and we infer that this requirement explains why S. aloides mainly grows in ponds, ditches and reed zones that are characterized by strong CO₂-supersaturation.     

At What Scales and Why Does Forest Structure Vary in Naturally Dynamic Boreal Forests? An Analysis of Forest Landscapes on Two Continents

Ecosystems - Identifying the scales of variation in forest structures and the underlying processes are fundamental for understanding forest dynamics. Here, we studied these scale-dependencies in...     

Differences in genitalia structure and function between subfamilies of longhorn beetles (Coleoptera: Cerambycidae)

Beetle genitalia are usually described only for taxonomic purposes without considering the possible function of structures. Exceptions are sporadic detailed studies on single species. We studied genital structures in the subfamilies of Cerambycidae and outlined assumptions on the function of these structures and the implications for the phylogeny of the Cerambycidae. We found that male genitalia in particular are taxon-specific on a higher taxonomic level; e.g., the parameres are widely variable in Cerambycinae, while in most Lamiinae species they appear relatively uniform and differ from those of the Cerambycinae. Internal sac structures are very different among the various subfamilies. Small backwards-pointing spines are the most common armature of the internal sac. The female genitalia are less variable, although ovipositor morphology may differ among subfamilies. In most species, the connection between the mates during copulation is achieved by the long internal sac and the ovipositor only, whereas the median lobe and parameres are in contact with the female abdomen only at the beginning of copulation. Cerambycinae and Lepturinae have a basal swelling of the endophallus to prevent it from sliding back into the male abdomen during copulation. The long internal sac functions in connecting the mates and guaranteeing the sperm transfer.     

Low translocation of Bacillus thuringiensis israelensis to inner organs in mice after pulmonary exposure to commercial biopesticide

Translocation of viable cells from a Bacillus thuringiensis israelensis-based biopesticide to inner organs in a mouse model was studied. Mice were exposed to the originally formulated product through the lungs and gastrointestinal tract by intratracheal instillation. Colony forming units (CFU) were grown from lungs, caecum, spleen and liver on Bacillus cereus-specific agar (BCSA) after 24 h and finally determined to be biopesticide strain B. t. israelensis by large plasmid profile. No CFU were found in spleen or liver of the control mice or in any aerosol background or material. We have shown that viable cells from the commercial product can translocate to spleen and liver of immunocompetent mice in a dose-dependent manner. Furthermore, we discuss the methods of exposure and how bacterial translocation should be taken into consideration when evaluating the safety of novel or reintroduced biopesticides in the future.