Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata

BACKGROUND: There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish. Orthology is even more problematic for intergenic regions of plant nuclear genomes, because plant genomes generally harbor a wealth of repetitive DNA. In theory orthologous intergenic data is valuable for studying rate variation because nucleotide substitutions in these regions should be under little selective constraint compared to coding regions. As a result, evolutionary rates in intergenic regions may more accurately reflect genomic features, like recombination and GC content, that contribute to nucleotide substitution. RESULTS: We generated a set of 66 intergenic sequences in Arabidopsis lyrata, a close relative of Arabidopsis thaliana. The intergenic regions included transposable element (TE) remnants and regions flanking the TEs. We verified orthology of these amplified regions both by comparison of existing A. lyrata – A. thaliana genetic maps and by using molecular features. We compared substitution rates among the 66 intergenic loci, which exhibit ~5-fold rate variation, and compared intergenic rates to a set of 64 orthologous coding sequences. Our chief observations were that the average rate of nucleotide substitution is slower in intergenic regions than in synonymous sites, that rate variation in both intergenic and coding regions correlate with GC content, that GC content alone is not sufficient to explain differences in rates between intergenic and coding regions, and that rates of evolution in intergenic regions correlate negatively with gene density. CONCLUSION: Our observations indicated that mutation rates vary among genomics regions as a function of base composition, suggesting that previous observations of "selective constraint" on non-coding regions could more accurately be attributed to a GC effect instead of selection. The negative correlation between nucleotide substitution rate and gene density provides a potential neutral explanation for a previously documented correlation between gene density and polymorphism levels within A. thaliana. Finally, we discuss potential forces that could contribute to rapid synonymous rates, and provide evidence to suggest that transcription-related mutation contributes to rate differences between intergenic and synonymous sites

A comparative computational analysis of nonautonomous Helitron elements between maize and rice

BackgroundHelitrons are DNA transposable elements that are proposed to replicate via a rolling circle mechanism. Non-autonomous helitron elements have captured gene fragments from many genes in maize (Zea mays ssp. mays) but only a handful of genes in Arabidopsis (Arabidopsis thaliana). This observation suggests very different histories for helitrons in these two species, but it is unclear which species contains helitrons that are more typical of plants.ResultsWe performed computational searches to identify helitrons in maize and rice genomic sequence data. Using 12 previously identified helitrons as a seed set, we identified 23 helitrons in maize, five of which were polymorphic among a sample of inbred lines. Our total sample of maize helitrons contained fragments of 44 captured genes. Twenty-one of 35 of these helitrons did not cluster with other elements into closely related groups, suggesting substantial diversity in the maize element complement. We identified over 552 helitrons in the japonica rice genome. More than 70% of these were found in a collinear location in the indica rice genome, and 508 clustered as a single large subfamily. The japonica rice elements contained fragments of only 11 genes, a number similar to that in Arabidopsis. Given differences in gene capture between maize and rice, we examined sequence properties that could contribute to differences in capture rates, focusing on 3' palindromes that are hypothesized to play a role in transposition termination. The free energy of folding for maize helitrons were significantly lower than those in rice, but the direction of the difference differed from our prediction.ConclusionMaize helitrons are clearly unique relative to those of rice and Arabidopsis in the prevalence of gene capture, but the reasons for this difference remain elusive. Maize helitrons do not seem to be more polymorphic among individuals than those of Arabidopsis; they do not appear to be substantially older or younger than the helitrons in either species; and our analyses provided little evidence that the 3' hairpin plays a role

Modeling payback from research into the efficacy of left-ventricular assist devices as destination therapy

Objectives: Ongoing developments in design have improved the outlook for left-ventricular assist device (LVAD) implantation as a therapy in end-stage heart failure. Nevertheless, early cost-effectiveness assessments, based on first-generation devices, have not been encouraging. Against this background, we set out (i) to examine the survival benefit that LVADs would need to generate before they could be deemed cost-effective; (ii) to provide insight into the likelihood that this benefit will be achieved; and (iii) from the perspective of a healthcare provider, to assess the value of discovering the actual size of this benefit by means of a Bayesian value of information analysis. Methods: Cost-effectiveness assessments are made from the perspective of the healthcare provider, using current UK norms for the value of a quality-adjusted life-year (QALY). The treatment model is grounded in published analyses of the Randomized Evaluation of Mechanical Assistance for the Treatment of Congestive Heart Failure (REMATCH) trial of first-generation LVADs, translated into a UK cost setting. The prospects for patient survival with second-generation devices is assessed using Bayesian prior distributions, elicited from a group of leading clinicians in the field. Results: Using established thresholds, cost-effectiveness probabilities under these priors are found to be low (.2 percent) for devices costing as much as £60,000. Sensitivity of the conclusions to both device cost and QALY valuation is examined. Conclusions: In the event that the price of the device in use would reduce to £40,000, the value of the survival information can readily justify investment in further trials

Kafirin structure and functionality

The structural and functional properties of kafirins are reviewed. Three classes of kafirin: the a, ß and ? forms have been identified at the protein level and one, the d, has been identified only at the gene and transcript levels. All forms show high homology with the equivalent zein proteins. By analogy with the zeins it is believed that the a-kafirins probably have an extended hairpin structure in solution, comprising elements of a-helix, ß-sheet and turns folded back on itself. Kafirins are the most hydrophobic of the prolamins as shown by their solubility, and calculated hydration free energies. The proteins exhibit extensive cross-linking by disulphide bonds and on cooking form indigestible aggregates which are not solubilised by reduction of disulphide bonds. In spite of continuing studies, the reasons for the low digestibility of the protein remain uncertain and there may be several factors involved. Other research has shown that kafirins may have non-food uses and may be used to form films

A VLT/NACO Study of Star Formation in the Massive Embedded Cluster RCW 38

We present adaptive optics (AO) near-infrared (JHKs) observations of the deeply embedded massive cluster RCW 38 using NACO on the VLT. Narrowband AO observations centered at wavelengths of 1.28, 2.12, and 2.17 micron were also obtained. The area covered by these observations is about 0.5 pc square, centered on the O star RCW 38 IRS2. We use the JHKs colors to identify young stars with infrared excess. Through a detailed comparison to a nearby control field, we find that most of the 337 stars detected in all three infrared bands are cluster members (~317), with essentially no contamination due to background or foreground sources. Five sources have colors suggestive of deeply embedded protostars, while 53 sources are detected at Ks only; their spatial distribution with respect to the extinction suggests they are highly reddened cluster members. Detectable Ks-band excess is found toward 29 +/- 3 % of the stars. For comparison to a similar area of Orion observed in the near-infrared, mass and extinction cuts are applied, and the excess fractions redetermined. The resulting excesses are then 25 +/- 5 % for RCW 38, and 42 +/- 8 % for Orion. RCW 38 IRS2 is shown to be a massive star binary with a projected separation of ~500 AU. Two regions of molecular hydrogen emission are revealed through the 2.12 micron imaging. One shows a morphology suggestive of a protostellar jet, and is clearly associated with a star only detected at H and Ks, previously identified as a highly obscured X-ray source. Three spatially extended cometary-like objects, suggestive of photoevaporating disks, are identified, but only one is clearly directly influenced by RCW 38 IRS2. A King profile provides a reasonable fit to the cluster radial density profile and a nearest neighbor distance analysis shows essentially no sub-clustering.Comment: 45 pages (17 figures), and full source table. Full resolution version available at http://www.cfa.harvard.edu/~bourke/rcw38

The twilight of the Liberal Social Contract? On the Reception of Rawlsian Political Liberalism

This chapter discusses the Rawlsian project of public reason, or public justification-based 'political' liberalism, and its reception. After a brief philosophical rather than philological reconstruction of the project, the chapter revolves around a distinction between idealist and realist responses to it. Focusing on political liberalism’s critical reception illuminates an overarching question: was Rawls’s revival of a contractualist approach to liberal legitimacy a fruitful move for liberalism and/or the social contract tradition? The last section contains a largely negative answer to that question. Nonetheless the chapter's conclusion shows that the research programme of political liberalism provided and continues to provide illuminating insights into the limitations of liberal contractualism, especially under conditions of persistent and radical diversity. The programme is, however, less receptive to challenges to do with the relative decline of the power of modern states

Constitutivism

A brief explanation and overview of constitutivism

Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis

Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) complex that catalyzes the metal-dependent maturation of the 5′ end of precursor tRNAs (pre-tRNAs) in all organisms. RNase P is comprised of a catalytic RNA (P RNA), and at least one essential protein (P protein). Although P RNA is the catalytic subunit of the enzyme and is active in the absence of P protein under high salt concentrations in vitro, the protein is still required for enzyme activity in vivo. Therefore, the function of the P protein and how it interacts with both P RNA and pre-tRNA have been the focus of much ongoing research. RNA-protein interactions in RNase P serve a number of critical roles in the RNP including stabilizing the structure, and enhancing the affinity for substrates and metal ions. This review examines the role of RNA-protein interactions in bacterial RNase P from both structural and mechanistic perspectives. © 2007 Wiley Periodicals, Inc. Biopolymers 87: 329–338, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57327/1/20846_ftp.pd

DESI Complete Calibration of the Color-Redshift Relation (DC3R2): Results from early DESI data

We present initial results from the Dark Energy Spectroscopic Instrument (DESI) Complete Calibration of the Color-Redshift Relation (DC3R2) secondary target survey. Our analysis uses 230k galaxies that overlap with KiDS-VIKING $ugriZYJHK_s$ photometry to calibrate the color-redshift relation and to inform photometric redshift (photo-z) inference methods of future weak lensing surveys. Together with Emission Line Galaxies (ELGs), Luminous Red Galaxies (LRGs), and the Bright Galaxy Survey (BGS) that provide samples of complementary color, the DC3R2 targets help DESI to span 56% of the color space visible to Euclid and LSST with high confidence spectroscopic redshifts. The effects of spectroscopic completeness and quality are explored, as well as systematic uncertainties introduced with the use of common Self Organizing Maps trained on different photometry than the analysis sample. We further examine the dependence of redshift on magnitude at fixed color, important for the use of bright galaxy spectra to calibrate redshifts in a fainter photometric galaxy sample. We find that noise in the KiDS-VIKING photometry introduces a dominant, apparent magnitude dependence of redshift at fixed color, which indicates a need for carefully chosen deep drilling fields, and survey simulation to model this effect for future weak lensing surveys.Comment: 19 pages, 16 figures, submitted to MNRAS, interactive visualizations at https://jmccull.github.io/DC3R2_Overvie

Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana

In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17–19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene×environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org