Progranulin haploinsufficiency causes biphasic social dominance abnormalities in the tube test

Loss‐of‐function mutations in progranulin (GRN) are a major autosomal dominant cause of frontotemporal dementia (FTD), a neurodegenerative disorder in which social behavior is disrupted. Progranulin‐insufficient mice, both Grn^+/? and Grn ^?/? , are used as models of FTD due to GRN mutations, with Grn^+/? mice mimicking the progranulin haploinsufficiency of FTD patients with GRN mutations. Grn^+/? mice have increased social dominance in the tube test at 6 months of age, although this phenotype has not been reported in Grn ^?/? mice. In this study, we investigated how the tube test phenotype of progranulin‐insufficient mice changes with age, determined its robustness under several testing conditions, and explored the associated cellular mechanisms. We observed biphasic social dominance abnormalities in Grn^+/? mice: at 6–8 months, Grn^+/? mice were more dominant than wild‐type littermates, while after 9 months of age, Grn^+/? mice were less dominant. In contrast, Grn ^?/? mice did not exhibit abnormal social dominance, suggesting that progranulin haploinsufficiency has distinct effects from complete progranulin deficiency. The biphasic tube test phenotype of Grn^+/? mice was associated with abnormal cellular signaling and neuronal morphology in the amygdala and prefrontal cortex. At 6–9 months, Grn^+/? mice exhibited increased mTORC2/Akt signaling in the amygdala and enhanced dendritic arbors in the basomedial amygdala, and at 9–16 months Grn^+/? mice exhibited diminished basal dendritic arbors in the prelimbic cortex. These data show a progressive change in tube test dominance in Grn^+/? mice and highlight potential underlying mechanisms by which progranulin insufficiency may disrupt social behavior.     

The role of protein complexes in human genetic disease

Many human genetic disorders are caused by mutations in protein‐coding regions of DNA. Taking protein structure into account has therefore provided key insight into the molecular mechanisms underlying human genetic disease. Although most studies have focused on the intramolecular effects of mutations, the critical role of the assembly of proteins into complexes is being increasingly recognized. Here, we review multiple ways in which consideration of protein complexes can help us to understand and explain the effects of pathogenic mutations. First, we discuss disorders caused by mutations that perturb intersubunit interactions in homomeric and heteromeric complexes. Second, we address how protein complex assembly can facilitate a dominant‐negative mechanism, whereby mutated subunits can disrupt the activity of wild‐type protein. Third, we show how mutations that change protein expression levels can lead to damaging stoichiometric imbalances. Finally, we review how mutations affecting different subunits of the same heteromeric complex often cause similar diseases, whereas mutations in different interfaces of the same subunit can cause distinct phenotypes.     

The distribution of fitness effects in an uncertain world

The distribution of fitness effects (DFE) among new mutations plays a critical role in adaptive evolution and the maintenance of genetic variation. Although fitness landscape models predict several key features of the DFE, most theory to date focuses on predictable environmental conditions, while ignoring stochastic environmental fluctuations that feature prominently in the ecology of many organisms. Here, we derive an extension of Fisher's geometric model that incorporates two common effects of environmental variation: (1) nonadaptive genotype‐by‐environment interactions (G × E), in which the phenotype of a given genotype varies across environmental contexts; and (2) random fluctuation of the fitness optimum, which generates fluctuating selection. We show that both factors cause a mismatch between the DFE within single generations and the distribution of geometric mean fitness effects (averaged over multiple generations) that governs long‐term evolutionary change. Such mismatches permit strong evolutionary constraints—despite an abundance of beneficial fitness variation within single environmental contexts—and to conflicting DFE estimates from direct versus indirect inference methods. Finally, our results suggest an intriguing parallel between the genetics and ecology of evolutionary constraints, with environmental fluctuations and pleiotropy placing qualitatively similar limits on the availability of adaptive genetic variation.     

Allelic composition and genetic background effects on transgene expression and inheritance in white clover

Allelic composition and genetic background effects on GUS expression and inheritance using a chimeric (cauliflower mosaic virus 35Sp:uidA) transgene were investigated in white clover as a prelude to transgenic cultivar development. Stable expression and Mendelian inheritance of the uidA transgene was observed over two generations when the uidA transgene was maintained in a heterozygous state. Transgenic backcross progeny (BC1) were intercrossed to produce segregating F2 populations. GUS-positive F2 plants were test-crossed with a non-transgenic control plant to determine whether individuals were heterozygous or homozygous for the transgene. Both expected and distorted segregation ratios were observed. Distortion of the segregation ratio was not caused by transgene inactivation or rearrangement, but was influenced by genetic background. BC1, BC2 and F2 populations were found to have similar levels of uidA gene expression. Quantification of GUS expression from progeny of high and low GUS expressing plants indicate that it is possible to alter transgene expression through selection. No difference was found between the level of expression for F2 plants homozygous or heterozygous for the transgene. These results indicate that F2 plants, homozygous for a transgene, might be used to develop a transgenic cultivar. However, progeny testing to determine the influence of genetic background is a prerequisite to such a development.     

Indirect genetic effects and the genetic bases of social dominance: evidence from cattle

Genetic studies of social behaviour have currently received new impetus from models including indirect genetic effects (IGEs) of social partners. This study aimed at investigating the contribution of conspecifics in social dominance, considered as response of dyadic interaction that is, winning (dominant individual) or losing (subordinate). A genetic correlation of −1 is expected between the attitude to win and the attitude to loose, and because a population always accounts for half winners and half losers, the heritability of the dominant status should be close to zero. Specifically, social dominance was studied in Aosta Chestnut and Aosta Black Pied (Bos taurus) breeds, alpine rustic cattle famous for traditional tournaments where pairs of cows assess dominant status in bloodless fights. The outcomes of 25 590 dyadic interactions performed by 8159 individuals in 11 years were analysed by applying a classical quantitative model and models including indirect effects. Data were analysed via Bayesian approach on a threshold trait. The assessment of variances revealed a genetic correlation of −0.976 between direct and indirect genetic components. The heritability measured on a liability scale was 0.122 for direct phenotype, but decreased to 0.014 when the total heritable variance (TBV) was considered. The trend of estimated breeding values showed that the total TBV was constant over the years, even though its direct component increased and the indirect part decreased. This result confirms the relevance of IGEs on social behaviour and the assumption that the mean individual social dominance cannot evolve within a population, due to the evolutionary constraints imposed by the ‘social environment''.     

Simultaneous MLPA-based multiplex point mutation and deletion analysis of the <Emphasis Type="Italic">Dystrophin</Emphasis> gene

The Multiplex Ligation-dependent Probe Amplification assay (MLPA) is the method of choice for the initial mutation screen in the analysis of a large number of genes where partial or total gene deletion is part of the mutation spectrum. Although MLPA dosage probes are usually designed to bind to normal DNA sequence to identify dosage imbalance, point mutation-specific MLPA probes can also be made. Using the dystrophin gene as a model, we have designed two MLPA probe multiplexes that are specific to a number of commonly listed point mutations in the Leiden dystrophin point mutation database (http://www.dmd.nl). The point mutation probes are designed to work simultaneously with two widely used dystrophin MLPA multiplexes, allowing both full dosage analysis and partial point mutation analysis in a single test. This approach may be adapted for other syndromes with well defined common point mutations or polymorphisms.     

The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana

Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.     

The correlation of substitution effects across populations and generations in the presence of nonadditive functional gene action

Allele substitution effects at quantitative trait loci (QTL) are part of the basis of quantitative genetics theory and applications such as association analysis and genomic prediction. In the presence of nonadditive functional gene action, substitution effects are not constant across populations. We develop an original approach to model the difference in substitution effects across populations as a first order Taylor series expansion from a “focal” population. This expansion involves the difference in allele frequencies and second-order statistical effects (additive by additive and dominance). The change in allele frequencies is a function of relationships (or genetic distances) across populations. As a result, it is possible to estimate the correlation of substitution effects across two populations using three elements: magnitudes of additive, dominance, and additive by additive variances; relationships (Nei’s minimum distances or Fst indexes); and assumed heterozygosities. Similarly, the theory applies as well to distinct generations in a population, in which case the distance across generations is a function of increase of inbreeding. Simulation results confirmed our derivations. Slight biases were observed, depending on the nonadditive mechanism and the reference allele. Our derivations are useful to understand and forecast the possibility of prediction across populations and the similarity of GWAS effects.     

Variability of Flavonol Contents during Floral Morphogenesis in the Poppy Papaver somniferum L.

We studied the contents of flavonols (kaempferol and quercetin) in the meristem of vegetative and generative apices of the main plant shoot in floral Papaver somniferum L. mutants, as well as in the normal plants at successive stages of flower development. Five stages of flower development were distinguished. Flavonols (kaempferol and quercetin) were present in all flower organs at all stages of floral morphogenesis we studied. However, their contents and distribution in different organs and at different stages of flower development markedly varied. No significant differences were found in the contents of flavonols in the meristems of vegetative and generative apices of the main shoot in the lines of floral mutants, as well as between the lines with different amounts of vegetative phytomeres. In the plants with normal flower structure, the contents of flavonols (kaempferol + quercetin) sharply increased with the beginning of differentiation of flower organs, i.e. from stage 3, to reach a maximum in the open flower, when gametogenesis is terminated and fertilization takes place. The level of flavonol contents in the petals (upper part) and stamen was at a maximum at all stages of flower development, while that in the gynaecium was at a minimum. The kaempferol : quercetin ratio was shifted towards quercetin at successive stages of flower development, most significantly in the stamens. The involvement of flavonols in the regulation of floral morphogenesis at stages of flower organs differentiation and functioning is discussed.     

Haploids adapt faster than diploids across a range of environments

Despite a great deal of theoretical attention, we have limited empirical data about how ploidy influences the rate of adaptation. We evolved isogenic haploid and diploid populations of Saccharomyces cerevisiae for 200 generations in seven different environments. We measured the competitive fitness of all ancestral and evolved lines against a common competitor and find that in all seven environments, haploid lines adapted faster than diploids, significantly so in three environments. We apply theory that relates the rates of adaptation and measured effective population sizes to the properties of beneficial mutations. We obtained rough estimates of the average selection coefficients in haploids between 2% and 10% for these first selected mutations. Results were consistent with semi-dominant to dominant mutations in four environments and recessive to additive mutations in two other environments. These results are consistent with theory that predicts haploids should evolve faster than diploids at large population sizes.     

Molecular genetic analysis of the intratumoral clonal heterogeneity of colorectal adenocarcinomas

Molecular genetic analysis of allelic deletions from the loci containing the tumor suppressor genes p16, p15, p19 (9p21), RB1 (13p14), PTEN (10q23), and TP53 (17p13); microsatellite instability; and activating mutations of K-RAS (codons 12 and 13) was performed in four different segments of sporadic colorectal cancer (CRC) in 11 patients. Intratumoral genetic heterogenity was detected in 9 out of 11 (81%) colorectal adenocarcinomas and was morphologically validated. Analysis of different segments of one tumor reported that not only intratumoral heterogeneity, but also the order of the appearance and distribution of molecular anomalies during tumorigenesis in sporadic CRC. K-RAS point mutations and anomalies of the p16-RB1-cyclin D pathway were assumed to occur prior to microsatellite instability and PTEN deletions during tumor progression.     

In vivo radiolabeling and turnover of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster: Gene dosage effects

In vivo radiolabeling of Drosophila melanogaster sn-glycerol-3-phosphate dehydrogenase (E.C. 1.1.1.8; GPDH) has been accomplished by microinjection of ³H-leucine into anesthetized flies. Comigration of immunoprecipitated radiolabeled GPDH with purified ¹⁴C-labeled GPDH-1 in SDS polyacrylamide disc gels has established the monospecificity of our immunoprecipitation technique. Short-term uptake experiments have demonstrated that maximum radiolabel incorporation of total TCA precipitable protein and immunoprecipitable GPDH-1 occurs within 4 hours postinjection, with GPDH-1 accounting for approximately 1% of the total radiolabeled TCA precipitable protein. In order to develop the parameters for turnover studies of GPDH in Drosophila, a comparative analysis of the rates of synthesis and degradation of GPDH-1 in flies bearing two and three doses of the structural gene have been conducted by the construction of adult flies aneuploid and euploid for the cytogenetic region 25F-26B on the left arm of chromosome II. Short-term uptake studies have demonstrated that the rate of GPDH-1 synthesis in the three-dose flies is approximately 1.58 times that found in the two-dose euploid flies. This value is in close agreement with data obtained for steady-state levels of CRM by rocket immunoelectrophoresis. In contrast, longterm pulse-chase experiments have revealed that rates of GPDH-1 degradation in these aneumploid and euploid flies appear to be identical. These data suggest that the rate of GPDH-1 synthesis in Drosophila is primarily regulated by a tightly linked cis-acting element which appears to act autonomously with respect to gene copy number as well as steady-state GPDH protein levels.     

Lack of nonadditive genetic effects on early fecundity in Drosophila melanogaster

Fecundity is usually considered as a trait closely connected to fitness and is expected to exhibit substantial nonadditive genetic variation and inbreeding depression. However, two independent experiments, using populations of different geographical origin, indicate that early fecundity in Drosophila melanogaster behaves as a typical additive trait of low heritability. The first experiment involved artificial selection in inbred and non-inbred lines, all of them started from a common base population previously maintained in the laboratory for about 35 generations. The realized heritability estimate was 0.151 +/- 0.075 and the inbreeding depression was very small and nonsignificant (0.09 +/- 0.09% of the non-inbred mean per 1% increase in inbreeding coefficient). With inbreeding, the observed decrease in the within-line additive genetic variance and the corresponding increase of the between-line variance were very close to their expected values for pure additive gene action. This result is at odds with previous studies showing inbreeding depression and, therefore, directional dominance for the same trait and species. All experiments, however, used laboratory populations, and it is possible that the original genetic architecture of the trait in nature was subsequently altered by the joint action of random drift and adaptation to captivity. Thus, we carried out a second experiment, involving inbreeding without artificial selection in a population recently collected from the wild. In this case we obtained, again, a maximum-likelihood heritability estimate of 0.210 +/- 0.027 and very little nonsignificant inbreeding depression (0.06 +/- 0.12%). The results suggest that, for fitness-component traits, low levels of additive genetic variance are not necessarily associated with large inbreeding depression or high levels of nonadditive genetic variance.