The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population

Although high-density SNP genotyping platforms generate a momentum for detailed genome-wide association (GWA) studies, an offshoot is a new insight into population genetics. Here, we present an example in one of the best-known founder populations by scrutinizing ten distinct Finnish early- and late-settlement subpopulations. By determining genetic distances, homozygosity, and patterns of linkage disequilibrium, we demonstrate that population substructure, and even individual ancestry, is detectable at a very high resolution and supports the concept of multiple historical bottlenecks resulting from consecutive founder effects. Given that genetic studies are currently aiming at identifying smaller and smaller genetic effects, recognizing and controlling for population substructure even at this fine level becomes imperative to avoid confounding and spurious associations. This study provides an example of the power of GWA data sets to demonstrate stratification caused by population history even within a seemingly homogeneous population, like the Finns. Further, the results provide interesting lessons concerning the impact of population history on the genome landscape of humans, as well as approaches to identify rare variants enriched in these subpopulations.     

The role of zooplankton grazing in the formation of `clear water phase' in a shallow charophyte-dominated lake

In Chara-dominated shallow eutrophic Lake Prossa (Estonia), the collapse of spring phytoplankton community occurred in late May after which both primary production (PP) and phytoplankton biomass (B&pinf;) stayed at a very low level. By mid-June the Secchi depth had increased up to 2.6 m indicating the achievement of the `clear water phase', which persisted thoughout the rest of the vegetation period. The biomass of `edible' phytoplankton formed on average 53% of the total phytoplankton biomass, and the share of herbivorous zooplankton was on average 61% of the total zooplankton biomass. In spring zooplankton removed daily 27% of the total B&pinf; and 29% of PP by grazing while in summer these values rarely exceeded 5%. Zooplankton grazing was responsible for the decrease of `edible' (<31 μm) phytoplankton after its spring peak as well as for maintaining its biomass at a very low level during the whole vegetation period. Depletion of mineral forms of nitrogen and phosphorus that occurred most probably because of the development of charophytes by the end of May supported the collapse of the whole phytoplankton community and kept the water clear throughout the summer and autumn.

     

Luciferase-based reporter system for in vitro evaluation of elongation rate and processivity of ribosomes

The elongation step of translation is a key contributor to the abundance, folding and quality of proteins and to the stability of mRNA. However, control over translation elongation has not been thoroughly investigated. In this study, a Renilla–firefly luciferase fusion reporter system was further developed to investigate the in vitro elongation rate and processivity of ribosomes independent of the initiation and termination steps. The reporter mRNA was constructed to contain a single ORF encoding in-frame Renilla luciferase, a specific domain moiety and firefly luciferase. Such a reporter structure enables the quantitative and individual evaluation of the synthesis of a specific domain. As a proof of principle, the synthesis of three protein domains of different lengths and structures was analyzed. Using a cell-free translation assay, both the elongation rate and processivity of ribosomes were shown to vary depending on the domain synthesized. Additionally, a stalling sequence consisting of ten rare arginine codons notably reduced the elongation rate and the processivity of the ribosomes. All these results are consistent with the previously known dynamics of elongation in vivo. Overall, the methodology presented in this report provides a framework for studying aspects that contribute to the elongation step of translation.     

Eveningness associates with smoking and sleep problems among pregnant women

Sleep problems during pregnancy impair maternal health and increase the risk for adverse pregnancy outcome. The circadian preference toward eveningness has been associated with sleep problems in previous studies. Here, we studied whether evening-type women had more sleep problems during their pregnancy, as compared with other chronotypes, in a sample consisting of 1653 pregnant women from the Finnish CHILD-SLEEP Birth Cohort. Chronotype was assessed with a shortened version of the morningness–eveningness questionnaire. Pregnant evening-type women reported more sleep problems, including troubles of falling asleep (OR = 3.4, p < 0.0001), poor sleep quality (OR = 2.9, p < 0.01) and daily tiredness (OR = 3.2, p < 0.0001) than the morning-type women, even after controlling for sleep duration and sleep deprivation. They had higher scores on Epworth Sleepiness Scale (p < 0.05), Basic Nordic Sleep Questionnaire (p < 0.0001) and Global Seasonality Score (p < 0.01) and were also more often smokers, also during pregnancy (p < 0.001) and reported poorer general health (p < 0.001) than the morning-type women. They also reported having had more sleep problems during their childhood (OR = 1.5, p < 0.05) and adolescence (OR = 2.0, p < 0.001) than the morning-type women. Our results indicate that eveningness is associated with more sleep problems and unhealthy life habits during pregnancy.     

Chromosome segregation and expression of rat immunoglobulins in rat/mouse hybrid myelomas

The chromosome segregation of hybrid myelomas from a fusion of rat immunized spleen cells and the mouse myeloma P3-X63-Ag8 has been analysed. Chromosome loss appears to be nonrandom. Most mouse chromosomes are retained. The rat chromosomes are preferentially lost but a few — particularly 1–5 and 13-are rarely lost. The specific retention of some rat chromosomes explains the stability of rat Ig expression in mouse-rat hybrids. Correlation of chromosome loss and retention and loss of rat heavy and light chains leads us to propose chromosome 14 as coding for the heavy chain.     

Systems pathology analysis identifies neurodegenerative nature of age‐related vitreoretinal interface diseases

Aging is a phenomenon that is associated with profound medical implications. Idiopathic epiretinal membrane (iEMR) and macular hole (MH) are the major vision‐threatening vitreoretinal diseases affecting millions of aging people globally, making these conditions an important public health issue. iERM is characterized by fibrous tissue developing on the surface of the macula, which leads to biomechanical and biochemical macular damage. MH is a small breakage in the macula and is associated with many ocular conditions. Although several individual factors and pathways are suggested, a systems pathology level understanding of the molecular mechanisms underlying these disorders is lacking. Therefore, we performed mass spectrometry‐based label‐free quantitative proteomics analysis of the vitreous proteomes from patients with iERM and MH to identify the key proteins, as well as the multiple interconnected biochemical pathways, contributing to the development of these diseases. We identified a total of 1,014 unique proteins, many of which are linked to inflammation and the complement cascade, revealing the inflammation processes in retinal diseases. Additionally, we detected a profound difference in the proteomes of iEMR and MH compared to those of diabetic retinopathy with macular edema and rhegmatogenous retinal detachment. A large number of neuronal proteins were present at higher levels in the iERM and MH vitreous, including neuronal adhesion molecules, nervous system development proteins, and signaling molecules, pointing toward the important role of neurodegenerative component in the pathogenesis of age‐related vitreoretinal diseases. Despite them having marked similarities, several unique vitreous proteins were identified in both iERM and MH, from which candidate targets for new diagnostic and therapeutic approaches can be provided.     

Unconstrained gene flow between populations of a widespread epiphytic lichen Usnea subfloridana (Parmeliaceae,Ascomycota) in Estonia

Few studies have investigated the genetic diversity of populations of common and widespread lichenized fungi using microsatellite markers, especially the relationships between different measures of genetic diversity and environmental heterogeneity. The main aim of our study was to investigate the population genetics of a widespread and mainly clonally reproducing Usnea subfloridana at the landscape scale, focusing on the comparison of lichen populations within hemiboreal forest stands. Particular attention has been paid to the genetic differentiation of lichen populations in two geographically distinct regions in Estonia and the relationships between forest characteristics and measures of genetic diversity. We genotyped 578 Usnea thalli from eleven lichen populations using seven specific fungal microsatellite markers. Measures of genetic diversity (allelic richness, Shannon's information index, Nei's unbiased genetic diversity, clonal diversity, the number of multilocus genotypes, the number of private alleles, and the minimum number of colonization events) were calculated and compared between Usnea populations. Shared haplotypes, gene flow and AMOVA analyses suggest that unconstrained gene flow and exchange of multilocus genotypes exist between the two geographically remote regions in Estonia. Stand age, mean circumference of the host tree, size of forest site and tree species composition did not show any significant influence on allelic richness, Shannon's information index, Nei's unbiased genetic diversity, clonal diversity, the number of private alleles, and the minimum number of colonization events of U. subfloridana populations. Therefore it was concluded that other factors of habitat heterogeneity could probably have a more significant effect on population genetics of U. subfloridana populations.     

Quantification of root water uptake in soil using X‐ray computed tomography and image‐based modelling

Spatially averaged models of root–soil interactions are often used to calculate plant water uptake. Using a combination of X‐ray computed tomography (CT) and image‐based modelling, we tested the accuracy of this spatial averaging by directly calculating plant water uptake for young wheat plants in two soil types. The root system was imaged using X‐ray CT at 2, 4, 6, 8 and 12 d after transplanting. The roots were segmented using semi‐automated root tracking for speed and reproducibility. The segmented geometries were converted to a mesh suitable for the numerical solution of Richards' equation. Richards' equation was parameterized using existing pore scale studies of soil hydraulic properties in the rhizosphere of wheat plants. Image‐based modelling allows the spatial distribution of water around the root to be visualized and the fluxes into the root to be calculated. By comparing the results obtained through image‐based modelling to spatially averaged models, the impact of root architecture and geometry in water uptake was quantified. We observed that the spatially averaged models performed well in comparison to the image‐based models with <2% difference in uptake. However, the spatial averaging loses important information regarding the spatial distribution of water near the root system.