ALBERT

Description: [1]  Thirty years of balloon-borne measurements over Boulder (40 ∘ N, 105 ∘ W) are used to investigate the water vapor trend in the tropopause region. This analysis extends previously published trends, usually focusing on altitudes greater than 16km, to lower altitudes. Two new concepts are applied: 1) Trends are presented in a thermal tropopause (TP) relative coordinate system from − 2km below to 10km above the TP. 2) Sonde profiles are selected according to TP height. Tropical (TP z  〉 14km), extratropical (TP z  〈 12km), and transitional air mass types (12km 〈 TP z  〈 14km), reveal three different water vapor reservoirs. The analysis based on these concepts reduces the dynamically–induced water vapor variability at the TP and principally favors refined water vapor trend studies in the upper troposphere and lower stratosphere. Nonetheless, this study showshow uncertain trends are at altitudes −2 to + 4km around the TP. This uncertainty in turn has an influence on the uncertainty and interpretation of water vapor radiative effects at the TP, which are locally estimated for the 30 year period to be of uncertain sign. The much discussed decrease in water vapor at the beginning of 2001 is not detectable between −2 to 2km around the TP. On lower stratospheric isentropes, the water vapor change at the beginning of 2001 is more intense for extratropical than for tropical air mass types. This suggests a possible link with changing dynamics above the jet stream such as changes in the shallow branch of the Brewer–Dobson circulation.

Description: [1]  Observations of SF 6 are used to quantify the mean time since air was in (“mean age” from) the northern hemisphere (NH) mid-latitude surface layer. The mean age is a fundamental property of tropospheric transport that can be used in theoretical studies and used to evaluate transport in comprehensive models. Comparisons of simulated SF 6 and an idealized clock tracer confirm that the time lag between the SF 6 mixing ratio at a given location and the NH mid-latitude surface provides an accurate estimate of the mean age. The ages calculated from surface SF 6 measurements show large meridional gradients in the tropics but weak gradients in the extratropics, with near zero ages at the surface north of 30 o N and ages around 1.4 yr south of 30 o S. Aircraft measurements show weak vertical age gradients in the lower-middle troposphere, with only slight increases of age with height in the NH and slight decreases with height in the SH. There are large seasonal variations in the age at tropical stations (annual amplitudes around 0.5-1.0 yr), with younger ages during northern winter, but only weak seasonal variations at higher latitudes. The seasonality and interannual variations in the tropics and southern hemisphere are related to changes in locations of tropical convection. There is qualitative agreement, in both spatial and temporal variations, between the simulated ages and observations. The model ages tend to be older than observed, with differences of ~0.2 yr in the northern hemisphere upper troposphere and throughout the southern hemisphere troposphere.

Description: When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (〈100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking.

Description: The nearly neutral theory predicts that small effective population size provides the conditions for weakened selection. This is postulated to explain why our genome is more "bloated" than that of, for example, yeast, ours having large introns and large intergene spacer. If a bloated genome is also an error prone genome might it, however, be the case that selection for error-mitigating properties is stronger in our genome? We examine this notion using splicing as an exemplar, not least because large introns can predispose to noisy splicing. We thus ask whether, owing to genomic decay, selection for splice error-control mechanisms is stronger, not weaker, in species with large introns and small populations. In humans much information defining splice sites is in cis- exonic motifs, most notably exonic splice enhancers (ESEs). These act as splice-error control elements. Here then we ask whether within and between-species intron size is a predictor of the commonality of exonic cis- splicing motifs. We show that, as predicted, the proportion of synonymous sites that are ESE-associated and under selection in humans is weakly positively correlated with the size of the flanking intron. In a phylogenetically controlled framework, we observe, also as expected, that mean intron size is both predicted by N e .μ and is a good predictor of cis- motif usage across species, this usage coevolving with splice site definition. Unexpectedly, however, across taxa intron density is a better predictor of cis -motif usage than intron size. We propose that selection for splice-related motifs is driven by a need to avoid decoy splice sites that will be more common in genes with many and large introns. That intron number and density predict ESE usage within human genes is consistent with this, as is the finding of intragenic heterogeneity in ESE density. As intronic content and splice site usage across species is also well predicted by N e .μ , the result also suggests an unusual circumstance in which selection (for cis- modifiers of splicing) might be stronger when population sizes are smaller, as here splicing is noisier, resulting in a greater need to control error-prone splicing.

Description: Shallow, subtidal waters of coastal embayments are the primary nursery habitats of juvenile Pacific cod through much of their range. However, the importance of these habitats to the Bering Sea population is poorly understood as the Bering Sea offers relatively little of this habitat. In this study, we examined the use of demersal and pelagic habitats in the southeast Bering Sea by age-0 Pacific cod. In 4 years of demersal beam trawling on the shelf at depths of 20–146 m, fish were most abundant along the Alaska Peninsula (AKP) at depths to 50 m. In addition, 1 year of spatially intensive beam trawl sampling was conducted at depths of 5–30 m in a nearshore focal area along the central AKP. In this survey, age-0 cod were more abundant along the open coastline than they were in two coastal embayments, counter to patterns observed in the Gulf of Alaska. Demersal sampling in 2012 was conducted synoptically with surveys of surface and subsurface waters over the continental shelf. Age-0 cod were captured in pelagic waters over the middle and outer shelf, with maximum catches occurring over depths of 60–80 m. The similar size distributions of fish in coastal-demersal and shelf-surface habitats and the proximity of concentrations in the two habitat types suggests that habitat use in the Bering Sea occurs along a gradient from coastal to pelagic. While capture efficiencies may differ among trawl types, trawl-based estimates of age-0 cod density in demersal waters along the AKP was 10 times that observed in the highest density pelagic-shelf habitats, demonstrating the importance of coastal nursery habitats in this population. Despite representing a much smaller habitat area, the coastal waters along the AKP appear an important nursery area and support a significant fraction of the age-0 Pacific cod in the Bering Sea.

Description: [1]  We analyse the relation between atmospheric temperature and water vapor - a fundamental component of the global climate system - for stratospheric water vapor (SWV). We compare measurements of SWV (and methane where available) over the period 1980–2011 from NOAA-FPH, SAGE II, HALOE, MLS/Aura, and ACE-FTS to model predictions based on troposphere-to-stratosphere transport from ERA-Interim, and temperatures from ERA-Interim, MERRA, CFSR, RATPAC, HadAT2 and RICHv1.5. All model predictions are dry biased. The interannual anomalies of the model predictions show periods of fairly regular oscillations, alternating with more quiescent periods and a few large-amplitude oscillations. They all agree well (correlation coefficients 0.9 and larger) with observations for higher-frequency variations (periods up to 2–3 years). Differences between SWV observations, and temperature data, respectively, render analysis of the model minus observation residual difficult. However, we find fairly well-defined periods of drifts in the residuals. For the 1980's model predictions differ most, and only the calculation with ERA-Interim temperatures is roughly within observational uncertainties. All model predictions show a drying relative to HALOE in the 1990's, followed by a moistening in the early 2000's. Drifts to NOAA-FPH are similar (but stronger), whereas no drift is present against SAGE II. As a result, the model calculations have a less pronounced drop in SWV in 2000 than HALOE. From the mid-2000's onwards, models and observations agree reasonably, and some differences can be traced to problems in the temperature data. These results indicate that both SWV and temperature data may still suffer from artefacts that need to be resolved in order to answer the question whether the large-scale flow and temperature field is sufficient to explain water entering the stratosphere.

Description: Although both genotypes with elevated mutation rate (mutators) and mobilization of insertion sequence (IS) elements have substantial impact on genome diversification, their potential interactions are unknown. Moreover, the evolutionary forces driving gradual accumulation of these elements are unclear: Do these elements spread in an initially transposon-free bacterial genome as they enable rapid adaptive evolution? To address these issues, we inserted an active IS 1 element into a reduced Escherichia coli genome devoid of all other mobile DNA. Evolutionary laboratory experiments revealed that IS elements increase mutational supply and occasionally generate variants with especially large phenotypic effects. However, their impact on adaptive evolution is small compared with mismatch repair mutator alleles, and hence, the latter impede the spread of IS-carrying strains. Given their ubiquity in natural populations, such mutator alleles could limit early phase of IS element evolution in a new bacterial host. More generally, our work demonstrates the existence of an evolutionary conflict between mutation-promoting mechanisms.

Description: [1]  We present measurements from the Water Vapor Millimeter-wave Spectrometer (WVMS) instruments at Table Mountain, California (34.4°N, 242.3°E), and Mauna Loa, Hawaii (19.5°N, 204.4°E), and highlight the extended altitude range of the measurements at these sites, which now provide measurements down to 26 km. We show that this extended altitude range has been acquired without disturbing the existing long-term WVMS data set at Mauna Loa. Validation of the successful transition is provided by comparing WVMS measurements with coincident satellite measurements from the Aura Microwave Limb Sounder (MLS), the Atmospheric Chemistry Experiment, and the Michelson Interferometer for Passive Atmospheric Sounding. At the lowest altitudes where WVMS measurements are possible, we also compare with frost-point hygrometer balloon measurements. The water vapor mixing ratios measured at 50 km over Mauna Loa are the highest ever reported in the WVMS (since 1996) or MLS (since 2004) time series. Particularly encouraging for the new 26 km WVMS measurements is that they indicate an increase between 2010 and 2011 that is comparable to that observed by other instruments. This shows that these measurements are sensitive to variations at this altitude and that the instrumental baseline remains stable.

Description: The Bering Sea and Gulf of Alaska support a number of commercially important flatfish fisheries. These high latitude ecosystems are predicted to be most immediately impacted by ongoing ocean acidification, but the range of responses by commercial fishery species has yet to be fully explored. In this study, we examined the growth responses of northern rock sole ( Lepidopsetta polyxystra ) eggs and larvae across a range of CO 2 levels (ambient to 1500 µatm) to evaluate the potential sensitivity to ocean acidification. Laboratory-spawned eggs and larvae were reared at 8°C in a flow-through culture system in which CO 2 levels were maintained via computer-controlled injection of CO 2 into a seawater conditioning tank. Overall, we observed only minor effects of elevated CO 2 level on sizes of northern rock sole larvae. Size at hatch differed among offspring from four different females, but there was no significant effect of CO 2 level on egg survival or size at hatch. In three separate larval growth trials, there was little effect of CO 2 level on growth rates through the first 28 d post-hatch (DPH). However, in the one trial extended to 60 DPH, fish reared at the highest CO 2 level had lower condition factors after 28 DPH, suggesting that larvae undergoing metamorphosis may be more sensitive to environmental hypercapnia than earlier pre-flexion stages. These results suggest that while early life stages of northern rock sole are less sensitive to ocean acidification than previously examined flatfish, they may be more sensitive to elevated CO 2 levels than a previously studied gadid with a similar geographic range.

Description: Where in genes do pathogenic mutations tend to occur and does this provide clues as to the possible underlying mechanisms by which single nucleotide polymorphisms (SNPs) cause disease? As splice-disrupting mutations tend to occur predominantly at exon ends, known also to be hot spots of cis -exonic splice control elements, we examine the relationship between the relative density of such exonic cis -motifs and pathogenic SNPs. In particular, we focus on the intragene distribution of exonic splicing enhancers (ESE) and the covariance between them and disease-associated SNPs. In addition to showing that disease-causing genes tend to be genes with a high intron density, consistent with missplicing, five factors established as trends in ESE usage, are considered: relative position in exons, relative position in genes, flanking intron size, splice sites usage, and phase. We find that more than 76% of pathogenic SNPs are within 3–69 bp of exon ends where ESEs generally reside, this being 13% more than expected. Overall from enrichment of pathogenic SNPs at exon ends, we estimate that approximately 20–45% of SNPs affect splicing. Importantly, we find that within genes pathogenic SNPs tend to occur in splicing-relevant regions with low ESE density: they are found to occur preferentially in the terminal half of genes, in exons flanked by short introns and at the ends of phase (0,0) exons with 3' non-"AGgt" splice site. We suggest the concept of the "fragile" exon, one home to pathogenic SNPs owing to its vulnerability to splice disruption owing to low ESE density.