Within the fold: assessing differential expression measures and reproducibility in microarray assays

BACKGROUND: 'Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed between query and reference samples. More accurate measures of differential expression and effective data-normalization strategies are required to identify high-confidence sets of genes with biologically meaningful changes in transcription. Further, the analysis of a large number of expression profiles is facilitated by a common reference sample, the construction of which must be carefully addressed. RESULTS: We carried out a series of 'self-self' hybridizations in which aliquots of the same RNA sample were labeled separately with Cy3 and Cy5 fluorescent dyes and co-hybridized to the same microarray. From this, we can analyze the intensity-dependent behavior of microarray data, define a statistically significant measure of differential expression that exploits the structure of the fluorescent signals, and measure the inherent reproducibility of the technique. We also devised a simple procedure for identifying and eliminating low-quality data for replicates within and between slides. We examine the properties required of a universal reference RNA sample and show how pooling a small number of samples with a diverse representation of expressed genes can outperform more complex mixtures as a reference sample. CONCLUSION: Analysis of cell-line samples can identify systematic structure in measured gene-expression levels. A general procedure for analyzing cDNA microarray data is proposed and validated. We show that pooled reference samples should be based not only on the expression of individual genes in each cell line but also on the expression levels of genes within cell lines

Urban–Rural Differences in Older Adult Depression: A Systematic Review and Meta-analysis of Comparative Studies

Context: Depression among older adults (aged 60 years or older) is a problem that could be exacerbated by global trends in urbanization and population aging. The study purpose was to assess whether urban, relative to rural, residence is associated with depression among older adults and whether associations differ in countries with developed versus developing economies. Evidence acquisition: In 2017, the authors identified and extracted information from comparative studies of urban–rural depression prevalence among older adults. Studies were identified in PubMed, PsychINFO, and Web of Science and limited to English language articles published after 1985. Eighteen studies met inclusion criteria. Random effects meta-analysis was conducted to produce weighted pooled ORs estimating the association between urban–rural residence and depression for all study participants (N=31,598) and sub-analyses were conducted for developed (n=12,728) and developing (n=18,870) countries. Evidence synthesis: Depression prevalence was significantly higher among urban residents in ten studies and significantly higher among rural residents in three studies (all three conducted in China). Associations between urban–rural residence and depression generally remained significant after adjusting for covariates. In developed countries, the odds of depression were significantly higher among urban than rural residents (pooled OR=1.44, 95% CI=1.10, 1.88). However, in developing countries, this association was not observed (pooled OR=0.91, 95% CI=0.46, 1.77). Conclusions: Converging trends of urbanization and population aging could increase the global burden of depression among older adults. The pathways through which urban–rural residence influences depression risk among older adults might differ by country context. Future research should focus on measuring variation in these contexts

Examining the possible impact of daily transport on depression among older adults using an agent-based model

_Objectives:_ Daily transport may impact depression risk among older adults through several pathways including facilitating the ability to meet basic needs, enabling and promoting contact with other people and nature, and promoting physical activity (e.g. through active transportation such as walking or walking to public transit). Both daily transport and depression are influenced by the neighborhood environment. To provide insights into how transport interventions may affect depression in older adults, we developed a pilot agent-based model to explore the contribution of daily transport and neighborhood environment to older adults’ depression in urban areas. _Method:_ The model includes about 18,500 older adults (i.e. agents) between the ages of 65 and 85 years old, living in a hypothetical city. The city has a grid space with a number of neighborhoods and locations. Key dynamic processes in the model include aging, daily transport use and feedbacks, and the development of depression. Key parameters were derived from US data sources. The model was validated using empirical studies. _Results:_ An intervention that combines a decrease in bus fares, shorter bus waiting times, and more bus lines and stations is most effective at reducing depression. Lower income groups are likely to be more sensitive to the public transit-oriented intervention. _Conclusion:_ Preliminary results suggest that promoting public transit use may be a promising strategy to increase daily transport and decrease depression. Our results may have implications for transportation policies and interventions to prevent depression in older adults

Depression and alcohol misuse among older adults: exploring mechanisms and policy impacts using agent-based modelling

Purpose: To: (1) explore how multi-level factors impact the longitudinal prevalence of depression and alcohol misuse among urban older adults (≥ 65 years), and (2) simulate the impact of alcohol taxation policies and targeted interventions that increase social connectedness among excessive drinkers, socially isolated and depressed older adults; both alone and in combination. Methods: An agent-based model was developed to explore the temporal co-evolution of depression and alcohol misuse prevalence among older adults nested in a spatial network. The model was based on Los Angeles and calibrated longitudinally using data from the Multi-Ethnic Study of Atherosclerosis. Results: Interventions with a social component targeting depressed and socially isolated older adults appeared more effective in curbing depression prevalence than those focused on excessive drinkers. Targeting had similar impacts on alcohol misuse, though the effects were marginal compared to those on depression. Alcohol taxation alone had little impact on either depression or alcohol misuse trajectories. Conclusions: Interventions that improve social connectedness may reduce the prevalence of depression among older adults. Targeting considerations could play an important role in determining the success of such efforts

Geometric Resonances in Bose-Einstein Condensates with Two- and Three-Body Interactions

We investigate geometric resonances in Bose-Einstein condensates by solving the underlying time-dependent Gross-Pitaevskii equation for systems with two- and three-body interactions in an axially-symmetric harmonic trap. To this end, we use a recently developed analytical method [Phys. Rev. A 84, 013618 (2011)], based on both a perturbative expansion and a Poincar\'e-Lindstedt analysis of a Gaussian variational approach, as well as a detailed numerical study of a set of ordinary differential equations for variational parameters. By changing the anisotropy of the confining potential, we numerically observe and analytically describe strong nonlinear effects: shifts in the frequencies and mode coupling of collective modes, as well as resonances. Furthermore, we discuss in detail the stability of a Bose-Einstein condensate in the presence of an attractive two-body interaction and a repulsive three-body interaction. In particular, we show that a small repulsive three-body interaction is able to significantly extend the stability region of the condensate.Comment: 27 pages, 13 figure

Cas3 is a limiting factor for CRISPR-Cas immunity in Escherichia coli cells lacking H-NS

Background: CRISPR-Cas systems provide adaptive immunity to mobile genetic elements in prokaryotes. In many bacteria, including E. coli, a specialized ribonucleoprotein complex called Cascade enacts immunity by “an interference reaction" between CRISPR encoded RNA (crRNA) and invader DNA sequences called “protospacers”. Cascade recognizes invader DNA via short “protospacer adjacent motif” (PAM) sequences and crRNA-DNA complementarity. This triggers degradation of invader DNA by Cas3 protein and in some circumstances stimulates capture of new invader DNA protospacers for incorporation into CRISPR as “spacers” by Cas1 and Cas2 proteins, thus enhancing immunity. Co-expression of Cascade, Cas3 and crRNA is effective at giving E. coli cells resistance to phage lysis, if a transcriptional repressor of Cascade and CRISPR, H-NS, is inactivated (Δhns). We present further genetic analyses of the regulation of CRISPR-Cas mediated phage resistance in Δhns E. coli cells. Results: We observed that E. coli Type I-E CRISPR-Cas mediated resistance to phage λ was strongly temperature dependent, when repeating previously published experimental procedures. Further genetic analyses highlighted the importance of culture conditions for controlling the extent of CRISPR immunity in E. coli. These data identified that expression levels of cas3 is an important limiting factor for successful resistance to phage. Significantly, we describe the new identification that cas3 is also under transcriptional control by H-NS but that this is exerted only in stationary phase cells. Conclusions: Regulation of cas3 is responsive to phase of growth, and to growth temperature in E. coli, impacting on the efficacy of CRISPR-Cas immunity in these experimental systems

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD

Hypertensive Disorders of Pregnancy and DNA Methylation in Newborns Findings From the Pregnancy and Childhood Epigenetics Consortium

Hypertensive disorders of pregnancy (HDP) are associated with low birth weight, shorter gestational age, and increased risk of maternal and offspring cardiovascular diseases later in life. The mechanisms involved are poorly understood, but epigenetic regulation of gene expression may play a part. We performed meta-analyses in the Pregnancy and Childhood Epigenetics Consortium to test the association between either maternal HDP (10 cohorts; n=5242 [cases=476]) or preeclampsia (3 cohorts; n=2219 [cases=135]) and epigenome-wide DNA methylation in cord blood using the Illumina HumanMethylation450 BeadChip. In models adjusted for confounders, and with Bonferroni correction, HDP and preeclampsia were associated with DNA methylation at 43 and 26 CpG sites, respectively. HDP was associated with higher methylation at 27 (63%) of the 43 sites, and across all 43 sites, the mean absolute difference in methylation was between 0.6% and 2.6%. Epigenome-wide associations of HDP with offspring DNA methylation were modestly consistent with the equivalent epigenome-wide associations of preeclampsia with offspring DNA methylation (R-2=0.26). In longitudinal analyses conducted in 1 study (n=108 HDP cases; 550 controls), there were similar changes in DNA methylation in offspring of those with and without HDP up to adolescence. Pathway analysis suggested that genes located at/near HDP-associated sites may be involved in developmental, embryogenesis, or neurological pathways. HDP is associated with offspring DNA methylation with potential relevance to development.Peer reviewe