Quantile-based permutation thresholds for quantitative trait Loci hotspots

Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key importance. One approach, randomly allocating observed QTL across the genomic locations separately by trait, implicitly assumes all traits are uncorrelated. Recently, an empirical test for QTL hotspots was proposed on the basis of the number of traits that exceed a predetermined LOD value, such as the standard permutation LOD threshold. The permutation null distribution of the maximum number of traits across all genomic locations preserves the correlation structure among the phenotypes, avoiding the detection of spurious hotspots due to nongenetic correlation induced by uncontrolled environmental factors and unmeasured variables. However, by considering only the number of traits above a threshold, without accounting for the magnitude of the LOD scores, relevant information is lost. In particular, biologically interesting hotspots composed of a moderate to small number of traits with strong LOD scores may be neglected as nonsignificant. In this article we propose a quantile-based permutation approach that simultaneously accounts for the number and the LOD scores of traits within the hotspots. By considering a sliding scale of mapping thresholds, our method can assess the statistical significance of both small and large hotspots. Although the proposed approach can be applied to any type of heritable high-volume omic data set, we restrict our attention to expression (e)QTL analysis. We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set.     

关于极限定理的一个新结果

设{X_n,n≥0}是可列非齐次马氏链,S_n(i_1,…,i_m,w)表示m元状态序组(i_1,…,i_m)在序列(X_1,…,X_m),(X_2,…,X_m 1)…,(X_n,…,X_n m-1)中出现的次数．本文通过利用{X_n,n≥O}在Wiener概率空间的一种实现,给出了关于S_n(i_1,…,i_m,w)的一个对任意可列非齐次马氏链普遍成立的强级限定理．     

Subcellular organization of N2-fixing nodules of cowpea (Vigna unguiculata) supplied with silicon

Summary Provision of silicon (0, 0.048, 0.096, 0.24, 0.48, and 0.96 g/1) in the form of silicic acid (H₄SiO₄) to nodulated cowpea plants(Vignia unguiculata [L.] Walp.) grown in liquid culture resulted in considerable changes in the internal organization of nodule structure. Compared to the control plants which received no added silicate, bacteroid numbers increased significantly (P ≤ 0.05) at silicate concentrations of both 0.096 and 0.48 g/1. The number of symbiosomes also increased by 3.2-fold at the silicate concentration of 0.96 g/1 compared to the control. In contrast, the size of bacteroids and symbiosomes decreased significantly (P ≤ 0.05) inside nodules of silicate-treated plants. The peribacteroid space was also decreased considerably (P ≤ 0.05) with the application of 0.096 and 0.96 g of silicate per liter to plants. However, the size of intercellular spaces adjacent to infected and uninfected interstitial cells within the nodule medulla increased significantly (P ≤ 0.05) at 0.096 g of silicate per liter followed by a sharply marked (P ≤ 0.05) decrease with each subsequent increase in silicate application. The result was a large decrease (P≤0.05) in the area of bacteria-infected tissue occupied by intercellular space at the highest silicate concentration, which was caused by a significant (P ≤ 0.05) increase in cell wall thickness. Our findings show that the positive effects of silicon on N₂ fixation might actually be due to an increased number of bacteroids and symbiosomes.     

Filtering processes in the assembly of plant communities: Are species presence and abundance driven by the same traits?

Question: Is the response of plant traits to environment at the community level similar when considering species abundance and when considering species presence only? Location: Mountain grasslands, central Argentina. Methods: We used data from 57 floristic samples, ordinated through DCCA along moisture and grazing gradients combined with trait values from 85 species (plant height, leaf area, leaf thickness leaf toughness and SLA). For each sample, we calculated the weighted average (considering species abundance) and the simple average (considering only species presence). Through multiple regressions we analysed how each average (dependent variable) responded to moisture and grazing (DCCA scores along Axes 1 and 2, respectively, as independent variables). Results: Weighted averages of all traits were significantly associated to both gradients, while simple averages did not always respond. In some cases the responses followed similar but weaker trends than the responses of weighted averages, but in other cases these responses were qualitatively different. Traits more associated with size (plant height, leaf area, leaf thickness) responded more consistently (similar trends for both averages) to grazing than to moisture, while traits more associated with plant resource acquisition (SLA, leaf toughness) responded more consistently to moisture than to grazing. Conclusion: The trait values and combinations which determine the probability of species presence are not necessary the same as those which determine their probability of becoming abundant. To understand community assembly rules, both species presence and species abundance should be taken into account as the result of different, although closely linked, filtering processes.     

Phenotypic selection and regulation of reproduction in different environments in wild barley

Plasticity of the phenotypic architecture of wild barley, Hordeum spontaneum, was studied in response to water and nutrient stress. Direct and indirect selection on several vegetative and reproductive traits was estimated and path analysis used to reveal how regulating pathways via maternal investment differed between environments. Vegetative traits displayed differential regulating effect on fitness across experimental environments: (1) increase in size was selected for under optimal conditions and under water stress, but not under nutrient stress; (2) allocation to root biomass was selected for under optimal conditions, but it had no effect under nutrient stress and was strongly selected against when water was limiting; (3) delayed onset of reproduction was selected under nutrient limitation whereas earlier onset was selected under water stress. The regulating effect of reproductive traits on final reproductive output also differed across treatments, operating either at the 'early' stage of plant development through varying the number of initiated spikelets per spike (no stress and water stress treatment) or at the 'late' developmental stage adjusting the fertile spikelet weight (no stress and nutrient stress treatment). Reproductive output was regulated via seed abortion under no stress and water stress treatments. Although the underlying mechanism of the regulation through abortion has yet to be discovered, the specific mechanism of abortion under water stress appears to be different from that under optimal conditions. Our results demonstrate that not only is the character architecture in wild barley plastic and sensitive to changing availability of water and nutrients, but the regulating mechanism of maternal investment is also environmentally sensitive.     

Changes in gravity inhibit lymphocyte locomotion through type I collagen

Summary Immunity relies on the circulation of lymphocytes through many different tissues including blood vessels, lymphatic channels, and lymphoid organs. The ability of lymphocytes to traverse the interstitium in both nonlymphoid and lymphoid tissues can be determined in vitro by assaying their capacity to locomote through Type I collagen. In an attempt to characterize potential causes of microgravity-induced immunosuppression, we investigated the effects of simulated microgravity on human lymphocyte function in vitro using a specialized rotating-wall vessel culture system developed at the Johnson Space Center. This very low shear culture system randomizes gravitational vectors and provides an in vitro approximation of microgravity. In the randomized gravity of the rotating-wall vessel culture system, peripheral blood lymphocytes did not locomote through Type I collagen, whereas static cultures supported normal movement. Although cells remained viable during the entire culture period, peripheral blood lymphocytes transferred to unit gravity (static culture) after 6 h in the rotating-wall vessel culture system were slow to recover and locomote into collagen matrix. After 72 h in the rotating-wall vessel culture system and an additional 72 h in static culture, peripheral blood lymphocytes did not recover their ability to locomote. Loss of locomotory activity in rotating-wall vessel cultures appears to be related to changes in the activation state of the lymphocytes and the expression of adhesion molecules. Culture in the rotating-wall vessel system blunted the ability of peripheral blood lymphocytes to respond to polyclonal activation with phytohemagglutinin. Locomotory response remained intact when peripheral blood lymphocytes were activated by anti-CD3 antibody and interleukin-2 prior to introduction into the rotating-wall vessel culture system. Thus, in addition to the systemic stress factors that may affect immunity, isolated lymphocytes respond to gravitational changes by ceasing locomotion through model interstitium. These in vitro investigations suggest that microgravity induces non-stress-related changes in cell function that may be critical to immunity. Preliminary analysis of locomotion in true microgravity revealed a substantial inhibition of cellular movement in Type I collagen. Thus, the rotating-wall vessel culture system provides a model for analyzing the microgravity-induced inhibition of lymphocyte locomotion and the investigation of the mechanisms related to lymphocyte movement.