Leveraging related health phenotypes for polygenic prediction of impulsive choice,impulsive action,and impulsive personality traits in 1534 European ancestry community adults

Impulsivity refers to a number of conceptually related phenotypes reflecting self-regulatory capacity that are considered promising endophenotypes for mental and physical health. Measures of impulsivity can be broadly grouped into three domains, namely, impulsive choice, impulsive action, and impulsive personality traits. In a community-based sample of ancestral Europeans (n = 1534), we conducted genome-wide association studies (GWASs) of impulsive choice (delay discounting), impulsive action (behavioral inhibition), and impulsive personality traits (UPPS-P), and evaluated 11 polygenic risk scores (PRSs) of phenotypes previously linked to self-regulation. Although there were no individual genome-wide significant hits, the neuroticism PRS was positively associated with negative urgency (adjusted R² = 1.61%, p = 3.6 × 10⁻⁷) and the educational attainment PRS was inversely associated with delay discounting (adjusted R² = 1.68%, p = 2.2 × 10⁻⁷). There was also evidence implicating PRSs of attention-deficit/hyperactivity disorder, externalizing, risk-taking, smoking cessation, smoking initiation, and body mass index with one or more impulsivity phenotypes (adjusted R²s: 0.35%–1.07%; FDR adjusted ps = 0.05–0.0006). These significant associations between PRSs and impulsivity phenotypes are consistent with established genetic correlations. The combined PRS explained 0.91%–2.46% of the phenotypic variance for individual impulsivity measures, corresponding to 8.7%–32.5% of their reported single-nucleotide polymorphism (SNP)-based heritability, suggesting a non-negligible portion of the SNP-based heritability can be recovered by PRSs. These results support the predictive validity and utility of PRSs, even derived from related phenotypes, to inform the genetics of impulsivity phenotypes.     

Tensor response quantile regression with neuroimaging data

Collecting neuroimaging data in the form of tensors (i.e. multidimensional arrays) has become more common in mental health studies, driven by an increasing interest in studying the associations between neuroimaging phenotypes and clinical disease manifestation. Motivated by a neuroimaging study of post-traumatic stress disorder (PTSD) from the Grady Trauma Project, we study a tensor response quantile regression framework, which enables novel analyses that confer a detailed view of the potentially heterogeneous association between a neuroimaging phenotype and relevant clinical predictors. We adopt a sensible low-rank structure to represent the association of interest, and propose a simple two-step estimation procedure which is easy to implement with existing software. We provide rigorous theoretical justifications for the intuitive two-step procedure. Simulation studies demonstrate good performance of the proposed method with realistic sample sizes in neuroimaging studies. We conduct the proposed tensor response quantile regression analysis of the motivating PTSD study to investigate the association between fMRI resting-state functional connectivity and PTSD symptom severity. Our results uncover non-homogeneous effects of PTSD symptoms on brain functional connectivity, which cannot be captured by existing tensor response methods.     

On generalized latent factor modeling and inference for high-dimensional binomial data

We explore a hierarchical generalized latent factor model for discrete and bounded response variables and in particular, binomial responses. Specifically, we develop a novel two-step estimation procedure and the corresponding statistical inference that is computationally efficient and scalable for the high dimension in terms of both the number of subjects and the number of features per subject. We also establish the validity of the estimation procedure, particularly the asymptotic properties of the estimated effect size and the latent structure, as well as the estimated number of latent factors. The results are corroborated by a simulation study and for illustration, the proposed methodology is applied to analyze a dataset in a gene–environment association study.     

珍稀濒危植物江南油杉群落乔木层主要树种种间关联性分析

基于2×2列联表,采用方差比率法(R_v)、x²检验、Pearson相关系数检验和Spearman秩相关系数检验等方法,对福建君子峰国家级自然保护区江南油杉(Keteleeria fortunei var. cyclolepis)群落乔木层主要树种进行种间关联性分析,并通过主成分分析(PCA)划分生态种组。结果表明,21种主要树种总体表现为不显著负关联,且江南油杉与其他物种多呈不显著相关。210个种对中,正相关的有110对,负相关的有81对,不相关的有19对,正负比1.36。绝大多数种对间呈不显著相关,显著率仅为0.48%,物种间相互独立。Pearson相关系数和Spearman秩相关系数检验结果具有一致性,负相关种对数大于正相关种对数,绝大多数种对不显著,显著率分别为6.19%和7.14%。与x²检验相比,Pearson相关系数和Spearman秩相关系数检验方式更加灵敏。运用PCA二维排序可将主要树种划分为4个生态种组,同一生态种组内物种的生态习性和资源需求相似,多呈正相关,种对间相互依赖共存;不同生态种组间物种多呈负...     

Armillaria jezoensis,a new symbiont ofGaleola septentrionalis (Orchidaceae) in Hokkaido

NineArmillaria isolates obtained from the roots ofGaleola septentrionalis in Hokkaido were identified asA. jezoensis by means of mating tests. Cultures of these isolates were similar in colony morphology, mycelial growth and rhizomorph formation on each of malt extract-dextrose agar (MDA), potato-dextrose agar (PDA), andG. septentrionalis root extractdextrose agar (GDA) media, showing better mycelial growth and rhizomorph formation on GDA medium.     

Evidence for a peptidoglycan envelope in the cyanelles of Glaucocystis nostochinearum Itzigsohn

Glaucocystis nostochinearum is a eukaryotic organism with chloroplasts that have usually been assumed to be cyanelles — i.e., endosymbiotic cyanobacteria. Previous attempts by others to support this assumption by demonstrating the presence of a limiting peptidoglycan envelope have been unsuccessful.In the present study disruption of intact Glaucocystis cells with a glass tissue homogenizer permitted the isolation of the uniquely-shaped cyanelles. That these cyanelles were lunited by a peptidoglycan-containing envelope was concluted from the following evidence: (1) stability of isolated cyanelles in distilled water as determined by the preservation of their intactness and peculiar asymmetrical shape; (2) lysozyme sensitivity as demonstrated by lysis of isolated cyanelles when treated with low concentrations of lysozyme; (3) inhibition of the lysozyme-mediated lysis by N-acetyl-glucosamine-2, a known competitive inhibitor of lysozyme, (4) visualization of a thin, electron dense layer between the two limiting membranes around the cyanelle, and (5) isolation and identification of the peptidoglycan-specific amino acid, diaminopimelic acid, from the cyanelles.     

The use of the Cole/Hurlbert C8 association coefficient in inverse ecological classification

Abstract. Inverse classification is routinely used in vegetation surveys to produce groups of sociologically similar species. However, no classification methods have been proposed specifically for this purpose, nor has any evaluation been made of the suitability of existing methodsforthe purpose. Anewvariant of Cluster Analysis is introduced, i. e. using the Cole/Hurlbert association measure C₈ as coefficient, and named for convenience Cole Cluster Analysis. This method, and four standard ones, were used on saltmarsh vegetational data from New Zealand. Ecophysiological data were obtained from salt-tolerance experiments. These data, and distributional information, were used as independent criteria against which to compare the inverse vegetation classifications. Information Analysis did not prove suitable for inverse analysis in this test. Nor did Cluster Analysis with the Simple Matching Coefficient or with Jaccard's coefficient. Indicator Species Analysis was more suitable, but the new Cole Cluster Analysis seemed the most effective on these data.     

Nucleolar organizing chromosomes ofRicinus

Summary Pachytene chromosome morphology was compared in nine races ofRicinus communis L. (2n = 20), using pollen mother cells (PMCs) and light microscopy. Of the ten bivalents, only the two possessing nucleolar organizing regions (NORs), chromosomes 2 and 7, exhibit structural variations among the races. The NORs are located in the short arms of these two chromosomes. Most of the observed structural variations affect these short arms, which are similar morphologically and consist largely of heterochromatic segments. The PMCs contain a single nucleolus and this is associated with the NOR of each of the two chromosomes at a particular frequency in each race. In eight races, a nucleolar constriction (NC) is present in either chromosome 2 or chromosome 7. In these races, the nucleolus is associated with the chromosome possessing an NC at a frequency of 100% and with the chromosome lacking an NC at a frequency ranging between 5.6 and 100%, depending upon the race. No microscopically visible NC is present in the ninth race. In this race, the nucleolus is associated with both chromosomes 2 and 7 at a frequency of 100%. The association of the nucleolus with a chromosome possessing an NC is at the NC and with a chromosome lacking an NC is at the terminal heterochromatic segment of the short arm. Several interpretations are offered to account for the variations in frequency of association between the nucleolus and each of the nucleolar organizing chromosomes. It is suggested that the two non-linked NORs have evolved through some intragenomic changes rather than polyploidy, that this species is highly intolerant to structural variations other than those occurring in or near the NORs, and that structural variations in the nucleolar organizing chromosomes are not associated with racial variations in plant phenotype.Paper of the Journal Series, New Jersey Agricultural Experiment Station     

Satellite association of the nucleolar chromosomes in a plant

Summary A method for preparing chromosomes that included enzyme maceration and subsequent flame-drying allowed us to easily detect satellite association in the mitotic cells ofNothoscordum fragrans (2 n=19), which has six acrocentric nucleolar chromosomes in its chromosome complement. Of 593 metaphase plates examined, approximately 60% had satellite association. The number of chromosomes involved in the association varied from two to six, and the incidence decreased as the number of chromosomes involved in the association increased. Comparison of the same chromosomes stained with Giemsa and subsequently with silver demonstrated that the nucleolar organizing regions (NORs) that responded almost negatively to Giemsa and positively to silver was responsible for satellite association. The nucleoli may strongly correlate with satellite association since persistent nucleoli associated with a few metaphase chromosomes were sometimes found and the nucleoli had a strong tendency to fuse with each other at interphase. Four types of acrocentric chromosomes could be discriminated on the basis of the bands negatively staining with Hoechst. All four types were involved in satellite association and there were significant deviations from the expectation for random participation in the association.     

Temperature dependence of fitness components in geographical populations of Drosophila melanogaster: changing the association between size and fitness

Contrary to the conventional wisdom 'bigger is better', evolution at high temperature invariably leads to small individuals in Drosophila melanogaster . Natural selection is known to be responsible, meaning that genotypes that are small because of adaptation to high temperature must have some temperature dependent fitness advantage. In this study we consider both preadult and adult fitness components, and show that large adults from a cold adapted population significantly outperform small adults from a warm adapted population only when tested at low temperature and low larval density. In all other conditions 'bigger is not necessarily better', meaning that environmental influences are capable of altering the association between size and fitness. Yet, 'smaller wasn't better either' under any condition, when considering the overall measure of fitness. Examination of individual fitness components revealed population by temperature interaction in preadult survival; this interaction is potentially capable of explaining the temperature specific advantage of small adult body size. At high temperature, the warm adapted population exhibits superior preadult survival while producing small adults. Geographical variation in adult body size seems to be the result of selection on larval growth and competitive strategies, resulting in alterations in the association between fitness components.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 717–725.