Population genetics of transgene containment

Several strategies have been proposed for creating transgenic cultivars from which transgene escape to wild relatives would seem unlikely; for example, to impede escape through pollen, a transgene could be inserted into chloroplast DNA (cpDNA), which in many crops is rarely transmitted through pollen. None of these strategies would be failsafe; for example, the rate of cpDNA transmission through pollen may be low but non‐zero in many crops. Here, we study how the probability distribution of escape time depends on the rates of pollen and seed flow from the crop to wild populations, the number and sizes of the wild populations, the selection coefficient for the transgene, and a leakage parameter characteristic of the strategy, for example, the rate of cpDNA transmission through pollen. We find that even with a leakage parameter as small as 10^?3, the probability of escape within as few as 10 generations could be appreciable.     

Single-Leaf Resolution of the Temporal Population Dynamics of Aureobasidium pullulans on Apple Leaves

The abundance of phylloplane microorganisms typically varies over several orders of magnitude among leaves sampled concurrently. Because the methods traditionally used to sample leaves are destructive, it has remained unclear whether this high variability is due to fixed differences in habitat quality among leaves or to asynchronous temporal variation in the microbial population density on individual leaves. We developed a novel semidestructive assay to repeatedly sample the same apple leaves from orchard trees over time by removing progressively more proximal ~1-cm-wide transverse segments. Aureobasidium pullulans densities were determined by standard leaf homogenization and plating procedures and were expressed as CFU per square centimeter of segment. The A. pullulans population densities among leaves were lognormally distributed. The variability in A. pullulans population densities among subsections of a given leaf was one-third to one-ninth the variability among whole leaves harvested concurrently. Sequential harvesting of leaf segments did not result in detectable changes in A. pullulans density on residual leaf surfaces. These findings implied that we could infer whole-leaf A. pullulans densities over time by using partial leaves. When this successive sampling regimen was applied over the course of multiple 7- to 8-day experiments, the among-leaf effects were virtually always the predominant source of variance in A. pullulans density estimates. Changes in A. pullulans density tended to be synchronous among leaves, such that the rank order of leaves arrayed with respect to A. pullulans density was largely maintained through time. Occasional periods of asynchrony were observed, but idiosyncratic changes in A. pullulans density did not contribute appreciably to variation in the distribution of populations among leaves. This suggests that persistent differences in habitat (leaf) quality are primarily responsible for the variation in A. pullulans density among leaves in nature.     

Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples

Interindividual variability in the epigenome has gained tremendous attention for its potential in pathophysiological investigation, disease diagnosis, and evaluation of clinical intervention. DNA methylation is the most studied epigenetic mark in epigenome-wide association studies (EWAS) as it can be detected from limited starting material. Infinium 450K methylation array is the most popular platform for high-throughput profiling of this mark in clinical samples, as it is cost-effective and requires small amounts of DNA. However, this method suffers from low genome coverage and errors introduced by probe cross-hybridization. Whole-genome bisulfite sequencing can overcome these limitations but elevates the costs tremendously. Methyl-Capture Sequencing (MC Seq) is an attractive intermediate solution to increase the methylome coverage in large sample sets. Here we first demonstrate that MC Seq can be employed using DNA amounts comparable to the amounts used for Infinium 450K. Second, to provide guidance when choosing between the 2 platforms for EWAS, we evaluate and compare MC Seq and Infinium 450K in terms of coverage, technical variation, and concordance of methylation calls in clinical samples. Last, since the focus in EWAS is to study interindividual variation, we demonstrate the utility of MC Seq in studying interindividual variation in subjects from different ethnicities.     

Responses of benthic algae to nutrient enrichment in a shallow lake: Linking community production,biomass, and composition

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Effects of pioneer shrubs on the recruitment of the fleshy‐fruited tree Olea europaea ssp. cuspidata in Afromontane savanna

Question: Is seedling recruitment of a fleshy‐fruited tree in degraded Afromontane savanna dependent on shelter from pioneer shrubs, and is shelter availability related to shrub traits? Location: Degraded montane savanna in northern Ethiopia (13°36′N, 39°21′E). Method: Nurse plants of Olea europaea ssp. cuspidata seedlings were recorded using T‐square plotless sampling and clustered according to shrub traits, using Ward's method after Principal Components Analysis. Facilitation was further examined through experimental planting and Kaplan‐Meier survival analysis. Results: Both in grazed and protected areas, Olea recruits were found exclusively under shrubs, primarily under Euclea racemosa although Acacia etbaica was more abundant. Olea recruitment is distributed randomly at landscape scale, but depends on shelter at patch scale. Shelter ability is related to shrub shape and species identity. Dense multi‐stemmed shrubs with a wide base and crown on a mulch‐rich mound are key recruitment foci. Euclea shrubs have these favoured traits and probably act as preferential perching sites for avian seed dispersers. Soil and organic matter accumulation under Euclea shrubs may also create favourable conditions for Olea germination and survival. Experimentally planted seedlings had a better chance for survival under Euclea. Conclusions: Olea regeneration is probably subject to both passive (disperser‐mediated) and active facilitation. Small changes of shrub traits can alter the suitability of a patch for Olea recruitment. Protection of shrubs can increase facilitation for seedlings, while pruning may reduce competition for saplings and thus enhance forest succession. Planting of raised Olea seedlings under Euclea shrubs in years with a good rainy season may further assist forest restoration.     

CONTINUING STUDIES ON THE SOUTH AMHERST DROSOPHILA MELANOGASTER NATURAL POPULATION DURING THE 1970'S AND 1980'S

Continuing investigations on the South Amherst Drosophila melanogaster natural population following the significant decline and recovery of lethal (le) and semilethal (sle) frequencies in the late 1960's (Ives, 1970) show that the population has been remarkably stable although it contains MR (male recombination) and/or P DNA elements (Kidwell et al., 1977a; Green, 1980). A 13-year study affirms that the lethals present are nonrandomly distributed along the second chromosome and deficient on the right; they differ significantly in distribution from spontaneous (Ives, 1973) and δ-induced lethals (Minamori and Ito, 1971). Between 1970 and 1977, a total of 4,083 second chromosomes from the Markert subpopulation were analyzed; 28.9% of the chromosomes were lethal and 7.25% were semilethal in homozygous condition. Frequencies are similar for early summer and late fall collections although the rate of allelism among lethals is significantly higher in early summer than in late fall. For the large fall (1970–1979) Porch site population, 2,519 second chromosomes were analyzed; 29.5% were lethal and 8.0% were sublethal as homozygotes; the rate of allelism among lethals was 1.50%. At Hockanum, 1977–1983, lethal and semilethal frequencies were lower; the rate of allelism among lethals was 1.43%. The chromosome map distribution of lethals does not change between summer and late fall at Markert. The overall distributions of lethals at the Markert and Hockanum sites are similar. In tests for male recombination (MR) activity in the population over a 6-year period, a total of 0.47% recombinants were observed; these were uniformly distributed along the second chromosome. Comparisons are made with other long studied D. melanogaster populations.     

Beyond “greening” and “browning”: Trends in grassland ground cover fractions across Eurasia that account for spatial and temporal autocorrelation

Grassland ecosystems cover up to 40% of the global land area and provide many ecosystem services directly supporting the livelihoods of over 1 billion people. Monitoring long-term changes in grasslands is crucial for food security, biodiversity conservation, achieving Land Degradation Neutrality goals, and modeling the global carbon budget. Although long-term grassland monitoring using remote sensing is extensive, it is typically based on a single vegetation index and does not account for temporal and spatial autocorrelation, which means that some trends are falsely identified while others are missed. Our goal was to analyze trends in grasslands in Eurasia, the largest continuous grassland ecosystems on Earth. To do so, we calculated Cumulative Endmember Fractions (annual sums of monthly ground cover fractions) derived from MODIS 2002–2020 time series, and applied a new statistical approach PARTS that explicitly accounts for temporal and spatial autocorrelation in trends. We examined trends in green vegetation, non-photosynthetic vegetation, and soil ground cover fractions considering their independent change trajectories and relations among fractions over time. We derived temporally uncorrelated pixel-based trend maps and statistically tested whether observed trends could be explained by elevation, land cover, SPEI3, climate, country, and their combinations, all while accounting for spatial autocorrelation. We found no statistical evidence for a decrease in vegetation cover in grasslands in Eurasia. Instead, there was a significant map-level increase in non-photosynthetic vegetation across the region and local increases in green vegetation with a concomitant decrease in soil fraction. Independent environmental variables affected trends significantly, but effects varied by region. Overall, our analyses show in a statistically robust manner that Eurasian grasslands have changed considerably over the past two decades. Our approach enhances remote sensing-based monitoring of trends in grasslands so that underlying processes can be discerned.     

Linkage analysis of 26 Canadian breast and breast-ovarian cancer families

We have examined 26 Canadian families with hereditary breast or ovarian cancer for linkage to markers flanking the BRCA1 gene on chromosome 17q12–q21. Of the 15 families that contain cases of ovarian cancer, 94% were estimated to be linked to BRCA1. In contrast, there was no overall evidence of linkage in the group of 10 families with breast cancer without ovarian cancer. A genetic recombinant in a breast-ovarian cancer family indicates a placement of BRCA1 telomeric to D17S776, and helps to define the region of assignment of the cancer susceptibility gene. Other cancers of interest that appeared in the BRCA1-linked families included primary peritoneal cancer, cancer of the fallopian tube, and malignant melanoma.     

Local Explanations of Landscape Patterns: Can Analytical Approaches Approximate Simulation Models of Spatial Processes?

Research over the last 100 years has demonstrated the importance of space for ecological processes. Given this importance, it may seem natural to start investigations into broad-scale ecological processes with a comprehensive, broad-scale spatial map. Here we argue that it may sometimes be possible to answer important questions about spatial processes using crude spatial information obtained when a comprehensive map is not available. To present our argument, we first develop a simple simulation model for a perennial plant reproducing and dying on a landscape with different arrangements of suitable and unsuitable sites. We then develop a simple, analytical approximation to predict the fraction of suitable sites that are occupied by the simulated plants. The analytical approximation summarizes the spatial map by using a single parameter that gives the probability that a site adjacent to a suitable site is suitable. Comparing the predictions of both approaches highlights three points: (a) The role of the spatial environment in ecological processes may play out at the local scale. Therefore, studying the local-scale processes may provide insights into landscape patterns. (b) The predictions from the analytical approximation fail noticeably when suitable sites are rare and are distributed randomly (rather than clumped) on the map. In these situations, patches of interconnected suitable sites are very small, and populations within small patches may go extinct via demographic stochasticity. This illustrates how analytical approximations can be used to identify cases when local-scale spatial processes are not sufficient to understand the ecological consequences of space. (c) For many natural systems, constructing the appropriate environmental map needed to study ecological processes is difficult or impossible. However, summary characteristics such as those employed by the analytical approximation may be estimated directly in nature. Therefore, even in the absence of an explicitly spatial broad-scale map, it may be possible to study spatial processes by understanding which local-scale characteristics of space are important. Received 5 May 1997; accepted 31 July 1997.     

Mixed type inhibition of the renal Na+/H+ antiporter by Li+ and amiloride. Evidence for a modifier site

We studied the interactions of Na+, Li+, and amiloride on the Na+/H+ antiporter in brush-border membrane vesicles from rabbit renal cortex. Cation-mediated collapse of an outwardly directed proton gradient (pHin = 6.0; pHout = 7.5) was monitored with the fluorescent amine, acridine orange. Proton efflux resulting from external addition of Na+ or Li+ exhibited simple saturation kinetics with Hill coefficients of 1.0. However, kinetic parameters for Na+ and Li+ differed (Km for Li+ = 1.2 +/- 0.1 mM; Km for Na+ = 14.3 +/- 0.8 mM; Vmax for Li+ = 2.40 +/- 0.07 fluorescence units/s/mg of protein; Vmax for Na+ = 7.10 +/- 0.24 fluorescence units/s/mg of protein). Inhibition of Na+/H+ exchange by Li+ and amiloride was also studied. Li+ inhibited the Na+/H+ antiporter by two mechanisms. Na+ and Li+ competed with each other at the cation transport site. However, when [Na+] was markedly higher than [Li+], [( Na+] = 90 mM; [Li+] less than 1 mM), we observed noncompetitive inhibition (Vmax for Na+/H+ exchange reduced by 25%). The apparent Ki for this noncompetitive inhibition was congruent to 50 microM. In addition, 2-30 mM intravesicular Li+, but not Na+, resulted in trans inhibition of Na+/H+ exchange. Amiloride was a mixed inhibitor of Na+/H+ exchange (Ki = 30 microM, Ki' = 90 microM) but was only a simple competitive inhibitor of Li+/H+ exchange (Ki = 10 microM). At [Li] = 1 mM and [amiloride] less than 100 microM, inhibition of Na+/H+ exchange by a combination of the two inhibitors was always less than additive. These results suggest the presence of a cation-binding site (separate from the cation-transport site) which could be a modifier site of the Na+/H+ antiporter.