The Variance of Identity-by-Descent Sharing in the Wright–Fisher Model

Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has recently become feasible, enabling a wide range of applications from phasing and imputation to demographic inference. Here, we study the distribution of IBD sharing in the Wright–Fisher model. Specifically, using coalescent theory, we calculate the variance of the total sharing between random pairs of individuals. We then investigate the cohort-averaged sharing: the average total sharing between one individual and the rest of the cohort. We find that for large cohorts, the cohort-averaged sharing is distributed approximately normally. Surprisingly, the variance of this distribution does not vanish even for large cohorts, implying the existence of “hypersharing” individuals. The presence of such individuals has consequences for the design of sequencing studies, since, if they are selected for whole-genome sequencing, a larger fraction of the cohort can be subsequently imputed. We calculate the expected gain in power of imputation by IBD and subsequently in power to detect an association, when individuals are either randomly selected or specifically chosen to be the hypersharing individuals. Using our framework, we also compute the variance of an estimator of the population size that is based on the mean IBD sharing and the variance in the sharing between inbred siblings. Finally, we study IBD sharing in an admixture pulse model and show that in the Ashkenazi Jewish population the admixture fraction is correlated with the cohort-averaged sharing.IN isolated populations, even purported unrelated individuals often share genetic material that is identical-by-descent (IBD). Traditionally, the term IBD sharing referred to coancestry at a single site (or autozygosity, in the case of a diploid individual) and was widely investigated as a measure of the degree of inbreeding in a population (Hartl and Clark 2006). Recent years have brought dramatic increases in the quantity and density of available genetic data and, together with new computational tools, these data have enabled the detection of IBD sharing of entire genomic segments (see, e.g., Purcell et al. 2007; Kong et al. 2008; Albrechtsen et al. 2009; Gusev et al. 2009; Browning and Browning 2011; Carr et al. 2011; Brown et al. 2012). The availability of IBD detection tools that are efficient enough to detect shared segments in large cohorts has resulted in numerous applications, from demographic inference (Davison et al. 2009; Palamara et al. 2012) and characterization of populations (Gusev et al. 2012a) to selection detection (Albrechtsen et al. 2010), relatedness detection and pedigree reconstruction (Huff et al. 2011; Kirkpatrick et al. 2011; Stevens et al. 2011; Henn et al. 2012), prioritization of individuals for sequencing (Gusev et al. 2012b), inference of HLA type (Setty et al. 2011), detection of haplotypes associated with a disease or a trait (Akula et al. 2011; Gusev et al. 2011; Browning and Thompson 2012), imputation (Uricchio et al. 2012), and phasing (Palin et al. 2011).Recently, some of us used coalescent theory to calculate several theoretical quantities of IBD sharing under a number of demographic histories. Then, shared segments were detected in real populations, and their demographic histories were inferred (Palamara et al. 2012). Here, we expand upon Palamara et al. (2012) to investigate additional aspects of the stochastic variation in IBD sharing. Specifically, we provide a precise calculation for the variance of the total sharing in the Wright–Fisher model, either between a random pair of individuals or between one individual and all others in the cohort.Understanding the variation in IBD sharing is an important theoretical characterization of the Wright–Fisher model, and additionally, it has several practical applications. For example, it can be used to calculate the variance of an estimator of the population size that is based on the sharing between random pairs. In a different domain, the variance in IBD sharing is needed to accurately assess strategies for sequencing study design, specifically, in prioritization of individuals to be sequenced. This is because imputation strategies use IBD sharing between sequenced individuals and genotyped, not-sequenced individuals to increase the number of effective sequences analyzed in the association study (Palin et al. 2011; Gusev et al. 2012b; Uricchio et al. 2012).In the remainder of this article, we first review the derivation of the mean fraction of the genome shared between two individuals (Palamara et al. 2012). We then calculate the variance of this quantity, using coalescent theory with recombination. We provide a number of approximations, one of which results in a surprisingly simple expression, which is then generalized to a variable population size and to the sharing of segments in a length range. We also numerically investigate the pairwise sharing distribution and provide an approximate fit. We then turn to the average total sharing between each individual and the entire cohort. We show that this quantity, which we term the cohort-averaged sharing, is approximately normally distributed, but is much wider than naively expected, implying the existence of hypersharing individuals. We consider several applications: the number of individuals needed to be sequenced to achieve a certain imputation power and the implications to disease mapping, inference of the population size based on the total sharing, and the variance of the sharing between siblings. We finally calculate the mean and the variance of the sharing in an admixture pulse model and show numerically that admixture results in a broader than expected cohort-averaged sharing. Therefore, large variance of the cohort-averaged sharing can indicate admixture. In the Ashkenazi Jewish population, we show that the cohort-averaged sharing is strongly anticorrelated with the fraction of European ancestry.     

Long-lasting inhibition of EGFR autophosphorylation in A549 tumor cells by intracellular accumulation of non-covalent inhibitors

In the present study, a small set of reversible or irreversible 4-anilinoquinazoline EGFR inhibitors was tested in A549 cells at early (1 h) and late (8 h) time points after inhibitor removal from culture medium. A combination of assays was employed to explain the observed long-lasting inhibition of EGFR autophosphorylation. We found that EGFR inhibition at 8 h can be due, besides to the covalent interaction of the inhibitor with Cys797, as for PD168393 (2) and its prodrug 4, to the intracellular accumulation of non-covalent inhibitors by means of an active cell uptake, as for 5 and 6. Compounds 5–6 showed similar potency and duration of inhibition of EGFR autophosphorylation as the covalent inhibitor 2, while being devoid of reactive groups forming covalent bonds with protein thiols.     

Small molecules interacting with α-synuclein: antiaggregating and cytoprotective properties

Curcumin, a dietary polyphenol, has shown a potential to act on the symptoms of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases, as a consequence of its antioxidant, anti-inflammatory and anti-protein aggregation properties. Unfortunately, curcumin undergoes rapid degradation at physiological pH into ferulic acid, vanillin and dehydrozingerone, making it an unlikely drug candidate. Here, we evaluated the ability of some curcumin by-products: dehydrozingerone (1), its O-methyl derivative (2), zingerone (3), and their biphenyl analogues (4–6) to interact with α-synuclein (AS), using CD and fluorescence spectroscopy. In addition, the antioxidant properties and the cytoprotective effects in rat pheochromocytoma (PC12) cells prior to intoxication with H₂O₂, MPP+ and MnCl₂ were examined while the Congo red assay was used to evaluate the ability of these compounds to prevent aggregation of AS. We found that the biphenyl zingerone analogue (6) interacts with high affinity with AS and also displays the best antioxidant properties while the biphenyl analogues of dehydrozingerone (4) and of O-methyl-dehydrozingerone (5) are able to partially inhibit the aggregation process of AS, suggesting the potential role of a hydroxylated biphenyl scaffold in the design of AS aggregation inhibitors.     

Quantifying High Resolution Transitional Breaks in Plant and Mammal Distributions at Regional Extent and Their Association with Climate,Topography and Geology

Objectives

We quantify spatial turnover in communities of 1939 plant and 59 mammal species at 2.5 km resolution across a topographically heterogeneous region in south-eastern Australia to identify distributional breaks and low turnover zones where multiple species distributions overlap. Environmental turnover is measured to determine how climate, topography and geology influence biotic turnover differently across a variety of biogeographic breaks and overlaps. We identify the genera driving turnover and confirm the versatility of this approach across spatial scales and locations.

Methods

Directional moving window analyses, rotated through 360°, were used to measure spatial turnover variation in different directions between gridded cells containing georeferenced plant and mammal occurrences and environmental variables. Generalised linear models were used to compare taxic turnover results with equivalent analyses for geology, regolith weathering, elevation, slope, solar radiation, annual precipitation and annual mean temperature, both uniformly across the entire study area and by stratifying it into zones of high and low turnover. Identified breaks and transitions were compared to a conservation bioregionalisation framework widely used in Australia.

Results/Significance

Detailed delineations of plant and mammal turnover zones with gradational boundaries denoted subtle variation in species assemblages. Turnover patterns often diverged from bioregion boundaries, though plant turnover adhered most closely. A prominent break zone contained either comparable or greater numbers of unique genera than adjacent overlaps, but these were concentrated in a small subsection relatively under-protected by conservation reserves. The environmental correlates of biotic turnover varied for different turnover zones in different subsections of the study area. Topography and temperature showed much stronger relationships with plant turnover in a topographically complex overlap, relative to a lowland overlap where weathering was most predictive. This method can quantify transitional turnover patterns from small to broad extents, at different resolutions for any location, and complements broad-scale bioregionalisation schemes in conservation planning.     

Comparison of the Hematological Profile of Elite Road Cyclists during the 2010 and 2012 GiroBio Ten-Day Stage Races and Relationships with Final Ranking

Cycling stage races are strenuous endurance events during which exercise-induced variations in hematological parameters are consistently observed. However, specific literature on such changes is scarce and published data have been derived from small samples of athletes. The aims of this study were: (1) to determine the hematological response to middle-term strenuous endurance; and (2) to determine whether a relationship exists between the athlete-specific hematological profile and final placement in a cycling stage race. The study population was male professional cyclists (n = 253) competing in the 2010 (n = 144) and 2012 (n = 109) GiroBio 10-day stage races. Blood draws taken before the start of the race, at mid-race, and at end-race were performed in strict compliance with academic and anti-doping pre-analytical warnings. Blood chemistry included white blood cell, red blood cell, hemoglobin concentration, hematocrit, mean corpuscular volume (MCV), mean hemoglobin content (MCH), mean corpuscular hemoglobin content (MCHC), platelets, and reticulocyte relative and absolute counts. Compared to baseline values, erythrocyte, hemoglobin, hematocrit, MCHC, platelet and reticulocyte counts were all consistently lower at mid-race, but returned to normal by race-end, while leukocytes were increased in the final phase. MCV increased during both events. MCH increased in the first part to then return to baseline in the 2012 race. The calculated OFF-score consistently decreased in the first half of the race before increasing, but remained lower than the baseline value. The trends of variation in hematological parameters were substantially similar in both events. There was an inverse, albeit weak, relationship between placement and erythrocyte, platelet, hemoglobin, hematocrit and OFF-score values in the 2010, but not in the 2012 race. In conclusion, the data confirm that, in this large series of elite road cyclists, the strenuous effort a rider sustains during a stage race induces appreciable changes in the hematological profile.     

Omega-3 Eicosapentaenoic Acid Decreases CD133 Colon Cancer Stem-Like Cell Marker Expression While Increasing Sensitivity to Chemotherapy

Colorectal cancer is the third leading cause of cancer-related death in the western world. In vitro and in vivo experiments showed that omega-3 polyunsaturated fatty acids (n-3 PUFAs) can attenuate the proliferation of cancer cells, including colon cancer, and increase the efficacy of various anticancer drugs. However, these studies address the effects of n-3 PUFAs on the bulk of the tumor cells and not on the undifferentiated colon cancer stem-like cells (CSLCs) that are responsible for tumor formation and maintenance. CSLCs have also been linked to the acquisition of chemotherapy resistance and to tumor relapse. Colon CSLCs have been immunophenotyped using several antibodies against cellular markers including CD133, CD44, EpCAM, and ALDH. Anti-CD133 has been used to isolate a population of colon cancer cells that retains stem cells properties (CSLCs) from both established cell lines and primary cell cultures. We demonstrated that the n-3 PUFA, eicosapentaenoic acid (EPA), was actively incorporated into the membrane lipids of COLO 320 DM cells. 25 uM EPA decreased the cell number of the overall population of cancer cells, but not of the CD133 (+) CSLCs. Also, we observed that EPA induced down-regulation of CD133 expression and up-regulation of colonic epithelium differentiation markers, Cytokeratin 20 (CK20) and Mucin 2 (MUC2). Finally, we demonstrated that EPA increased the sensitivity of COLO 320 DM cells (total population) to both standard-of-care chemotherapies (5-Fluorouracil and oxaliplatin), whereas EPA increased the sensitivity of the CD133 (+) CSLCs to only 5-Fluorouracil.     

Apolipoprotein(a) Kringle-IV Type 2 Copy Number Variation Is Associated with Venous Thromboembolism

In addition to the established association between high lipoprotein(a) [Lp(a)] concentrations and coronary artery disease, an association between Lp(a) and venous thromboembolism (VTE) has also been described. Lp(a) is controlled by genetic variants in LPA gene, coding for apolipoprotein(a), including the kringle-IV type 2 (KIV-2) size polymorphism. Aim of the study was to investigate the role of LPA gene KIV-2 size polymorphism and single nucleotide polymorphisms (SNPs) (rs1853021, rs1800769, rs3798220, rs10455872) in modulating VTE susceptibility. Five hundred and sixteen patients with VTE without hereditary and acquired thrombophilia and 1117 healthy control subjects, comparable for age and sex, were investigated. LPA KIV-2 polymorphism, rs3798220 and rs10455872 SNPs were genotyped by TaqMan technology. Concerning rs1853021 and rs1800769 SNPs, PCR-RFLP assay was used. LPA KIV-2 repeat number was significantly lower in patients than in controls [median (interquartile range) 11(6–17) vs 15(9–25), p<0.0001]. A significantly higher prevalence of KIV-2 repeat number ≤7 was observed in patients than in controls (33.5% vs 15.5%, p<0.0001). KIV-2 repeat number was independently associated with VTE (p = 4.36 x10^-9), as evidenced by the general linear model analysis adjusted for transient risk factors. No significant difference in allele frequency for all SNPs investigated was observed. Haplotype analysis showed that LPA haplotypes rather than individual SNPs influenced disease susceptibility. Receiver operating characteristic curves analysis showed that a combined risk prediction model, including KIV-2 size polymorphism and clinical variables, had a higher performance in identifying subjects at VTE risk than a clinical-only model, also separately in men and women.     

An Optimal Frequency in Ca2+ Oscillations for Stomatal Closure Is an Emergent Property of Ion Transport in Guard Cells

Oscillations in cytosolic-free Ca²⁺ concentration ([Ca2+]_i) have been proposed to encode information that controls stomatal closure. [Ca2+]_i oscillations with a period near 10 min were previously shown to be optimal for stomatal closure in Arabidopsis (Arabidopsis thaliana), but the studies offered no insight into their origins or mechanisms of encoding to validate a role in signaling. We have used a proven systems modeling platform to investigate these [Ca2+]_i oscillations and analyze their origins in guard cell homeostasis and membrane transport. The model faithfully reproduced differences in stomatal closure as a function of oscillation frequency with an optimum period near 10 min under standard conditions. Analysis showed that this optimum was one of a range of frequencies that accelerated closure, each arising from a balance of transport and the prevailing ion gradients across the plasma membrane and tonoplast. These interactions emerge from the experimentally derived kinetics encoded in the model for each of the relevant transporters, without the need of any additional signaling component. The resulting frequencies are of sufficient duration to permit substantial changes in [Ca2+]_i and, with the accompanying oscillations in voltage, drive the K⁺ and anion efflux for stomatal closure. Thus, the frequency optima arise from emergent interactions of transport across the membrane system of the guard cell. Rather than encoding information for ion flux, these oscillations are a by-product of the transport activities that determine stomatal aperture.Stomata in the leaf epidermis are the main pathway both for CO₂ entry for photosynthesis and for foliar water loss by transpiration. Guard cells surround the stomatal pore and regulate the aperture, balancing the often conflicting demands for CO₂ and water conservation. Guard cells open and close the pore by expanding and contracting through the uptake and loss, respectively, of osmotic solutes, notably of K⁺, Cl⁻, and malate²⁻ (Mal²⁻; Pandey et al., 2007; Kim et al., 2010; Roelfsema and Hedrich, 2010; Lawson and Blatt, 2014). These transport processes comprise the final effectors of a regulatory network that coordinates transport across the plasma membrane and tonoplast, and maintains the homeostasis of the guard cell. A number of well-defined signals—including light, CO₂, drought and the water stress hormone abscisic acid (ABA)—act on this network, altering transport, solute content, turgor and cell volume, and ultimately stomatal aperture.Much research has focused on stomatal closure, underscoring both Ca²⁺-independent and Ca²⁺-dependent signaling. Of the latter, elevated cytosolic-free Ca²⁺ concentration ([Ca2+]_i) inactivates inward-rectifying K⁺ channels (I_K,in) to prevent K⁺ uptake and activates Cl⁻ (anion) channels (I_Cl) at the plasma membrane to depolarize the membrane and engage K⁺ efflux through outward-rectifying K⁺ channels (I_K,out; Keller et al., 1989; Blatt et al., 1990; Thiel et al., 1992; Lemtiri-Chlieh and MacRobbie, 1994). ABA, and most likely CO₂ (Kim et al., 2010), elevate [Ca2+]_i by facilitating Ca²⁺ entry at the plasma membrane to trigger Ca²⁺ release from endomembrane stores, a process often described as Ca²⁺-induced Ca²⁺ release (Grabov and Blatt, 1998, 1999). The hormone promotes Ca²⁺ influx by activating Ca²⁺ channels (I_Ca) at the plasma membrane, even in isolated membrane patches (Hamilton et al., 2000, 2001), which is linked to reactive oxygen species (Kwak et al., 2003; Wang et al., 2013). In parallel, cADP-ribose and nitric oxide promote endomembrane Ca²⁺ release and [Ca2+]_i elevation (Leckie et al., 1998; Neill et al., 2002; Garcia-Mata et al., 2003; Blatt et al., 2007). Best estimates indicate that endomembrane release accounts for more than 95% of the Ca²⁺ entering the cytosol to raise [Ca2+]_i (Chen et al., 2012; Wang et al., 2012).One feature of stomatal response to ABA, and indeed to a range of stimuli both hormonal as well as external, is its capacity for oscillations both in membrane voltage and [Ca2+]_i. Guard cell [Ca2+]_i at rest is typically around 100 to 200 nm, as it is in virtually all living cells. In response to ABA, [Ca2+]_i can rise above 1 μm—and locally, most likely above 10 μm—often in cyclic transients of tens of seconds to several minutes’ duration in association with oscillations in voltage and stomatal closure (Gradmann et al., 1993; McAinsh et al., 1995; Webb et al., 1996; Grabov and Blatt, 1998, 1999; Staxen et al., 1999; Allen et al., 2001). In principle, cycling in voltage and [Ca2+]_i arises as closure is accelerated with a controlled release of K⁺, Cl⁻, and Mal²⁻ from the guard cell and is subject to extracellular ion concentrations (Gradmann et al., 1993; Chen et al., 2012). However, it has been proposed that these, and similar oscillations in a variety of plant cell models, serve as physiological signals in their own right (McAinsh et al., 1995; Ehrhardt et al., 1996; Taylor et al., 1996). In support of such a signaling role, experiments designed to impose [Ca2+]_i (and voltage) oscillations in guard cells have yielded an optimal frequency for closure with a period near 10 min (Allen et al., 2001). Nonetheless, the studies offer no mechanistic explanation for this optimum that could validate a causal role in signaling, and none has been forthcoming since. Here we address questions of how such optimal frequencies in [Ca2+]_i oscillation arise and their relevance for stomatal closure, using quantitative systems analysis of guard cell transport and homeostasis. Our findings indicate that oscillations in voltage and [Ca2+]_i, and their optima associated with stomatal closure, are most simply explained as emerging from the interactions between ion transporters that drive stomatal closure. Thus, we conclude that these oscillations do not control, but are a by-product of the transport that determines stomatal aperture.