Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii

<p>Abstract</p> <p>Background</p> <p>The holoparasitic plant genus <it>Cuscuta </it>comprises species with photosynthetic capacity and functional chloroplasts as well as achlorophyllous and intermediate forms with restricted photosynthetic activity and degenerated chloroplasts. Previous data indicated significant differences with respect to the plastid genome coding capacity in different <it>Cuscuta </it>species that could correlate with their photosynthetic activity. In order to shed light on the molecular changes accompanying the parasitic lifestyle, we sequenced the plastid chromosomes of the two species <it>Cuscuta reflexa </it>and <it>Cuscuta gronovii</it>. Both species are capable of performing photosynthesis, albeit with varying efficiencies. Together with the plastid genome of <it>Epifagus virginiana</it>, an achlorophyllous parasitic plant whose plastid genome has been sequenced, these species represent a series of progression towards total dependency on the host plant, ranging from reduced levels of photosynthesis in <it>C. reflexa </it>to a restricted photosynthetic activity and degenerated chloroplasts in <it>C. gronovii </it>to an achlorophyllous state in <it>E. virginiana</it>.</p> <p>Results</p> <p>The newly sequenced plastid genomes of <it>C. reflexa </it>and <it>C. gronovii </it>reveal that the chromosome structures are generally very similar to that of non-parasitic plants, although a number of species-specific insertions, deletions (indels) and sequence inversions were identified. However, we observed a gradual adaptation of the plastid genome to the different degrees of parasitism. The changes are particularly evident in <it>C. gronovii </it>and include (a) the parallel losses of genes for the subunits of the plastid-encoded RNA polymerase and the corresponding promoters from the plastid genome, (b) the first documented loss of the gene for a putative splicing factor, MatK, from the plastid genome and (c) a significant reduction of RNA editing.</p> <p>Conclusion</p> <p>Overall, the comparative genomic analysis of plastid DNA from parasitic plants indicates a bias towards a simplification of the plastid gene expression machinery as a consequence of an increasing dependency on the host plant. A tentative assignment of the successive events in the adaptation of the plastid genomes to parasitism can be inferred from the current data set. This includes (1) a loss of non-coding regions in photosynthetic <it>Cuscuta </it>species that has resulted in a condensation of the plastid genome, (2) the simplification of plastid gene expression in species with largely impaired photosynthetic capacity and (3) the deletion of a significant part of the genetic information, including the information for the photosynthetic apparatus, in non-photosynthetic parasitic plants.</p

Plastid located WHIRLY1 enhances the responsiveness of Arabidopsis seedlings toward abscisic acid

WHIRLY1 is a protein that can be translocated from the plastids to the nucleus, making it an ideal candidate for communicating information between these two compartments. Mutants of Arabidopsis thaliana lacking WHIRLY1 (why1) were shown to have a reduced sensitivity toward salicylic acid (SA) and abscisic acid (ABA) during germination. Germination assays in the presence of abamine, an inhibitor of ABA biosynthesis, revealed that the effect of SA on germination was in fact caused by a concomitant stimulation of ABA biosynthesis. In order to distinguish whether the plastid or the nuclear isoform of WHIRLY1 is adjusting the responsiveness toward ABA, sequences encoding either the complete WHIRLY1 protein or a truncated form lacking the plastid transit peptide were overexpressed in the why1 mutant background. In plants overexpressing the full-length sequence, WHIRLY1 accumulated in both plastids and the nucleus, whereas in plants overexpressing the truncated sequence, WHIRLY1 accumulated exclusively in the nucleus. Seedlings containing recombinant WHIRLY1 in both compartments were hypersensitive toward ABA. In contrast, seedlings possessing only the nuclear form of WHIRLY1 were as insensitive toward ABA as the why1 mutants. ABA was furthermore shown to lower the rate of germination of wildtype seeds even in the presence of abamine which is known to inhibit the formation of xanthoxin, the plastid located precursor of ABA. From this we conclude that plastid located WHIRLY1 enhances the responsiveness of seeds toward ABA even when ABA is supplied exogenously

Torsion pairs and rigid objects in tubes

We classify the torsion pairs in a tube category and show that they are in bijection with maximal rigid objects in the extension of the tube category containing the Pruefer and adic modules. We show that the annulus geometric model for the tube category can be extended to the larger category and interpret torsion pairs, maximal rigid objects and the bijection between them geometrically. We also give a similar geometric description in the case of the linear orientation of a Dynkin quiver of type A.Comment: 25 pages, 13 figures. Paper shortened. Minor errors correcte

Evaluation of a questionnaire to assess selected infectious diseases and their risk factors: Findings of a multicenter study

Background/objectives The risk to die from an infectious disease in Germany has been continuously decreasing over the last century. Since infections are, however, not only causes of death but risk factors for diseases like cardiovascular diseases, it is essential to monitor and analyze their prevalence and frequency, especially in consideration of the increased life expectancy. To gain more knowledge about infectious diseases as risk factors and their implications on the condition and change of the immune status, the German National Cohort (GNC), a population-based prospective cohort study, will recruit 200,000 subjects between 2014 and 2017. In Pretest 1, a feasibility study for the GNC, we evaluated a self-administered and self-report questionnaire on infectious diseases and on the use of health care facilities (hereinafter called “ID Screen”) for feasibility and validity. Methods: From August–November 2011, 435 participants between the ages of 20–69 completed the ID Screen. All subjects had been recruited via a random sample from the local residents’ registration offices by 4 of the 18 participating study centers. The questionnaire encompasses 77 variables in six sections assessing items such as 12-month prevalence of infections, cumulative prevalence of infectious diseases, visit of health care facilities and vaccination. The feasibility was amongst others evaluated by assessing the completeness and comprehensiveness of the questionnaire. To assess the questionnaires ability to measure “immune status” and “susceptibility to infections”, multivariate analysis was used. Results: The overall practicability was good and most items were well understood, demonstrated by 5 % of missing values. However, direct comparison of the items 12-month prevalence and lifetime prevalence of nephritis/pyelitis showed poor agreement and thereby poor understanding by 80 % of the participants, illustrating the necessity for a clear, lay person appropriate description of rare diseases to increase comprehensibility. The questionnaire will be used to support the assessment of immune dysfunction and frequency of infection. An analysis of these constructs in an exploratory factor analysis revealed limited applicability due to low interitem correlation (Cronbach’s α < 0.5). This is corroborated by the extraction of more than one factor with a Kaiser–Meyer–Olkin measure of 0.6 instead of a unidimensional latent construct for “immune status”. Conclusion: All in all, the ID Screen is a good and reliable tool to measure infectious diseases as risk factors and outcome in general, but requires a better translation of infection specific terms into lay person terms. For the assessment of the overall immune status, the tool has strong limitations. Vaccinations status should also rather be assessed based on vaccination certificates than on participants’ recall. Electronic supplementary material The online version of this article (doi: 10.1007/s00103-014-2052-y) contains supplementary material, which is available to authorized users

The emission by dust and stars of nearby galaxies in the Herschel KINGFISH survey

Using new far-infrared imaging from the Herschel Space Observatory with ancillary data from ultraviolet (UV) to submillimeter wavelengths, we estimate the total emission from dust and stars of 62 nearby galaxies in the KINGFISH survey in a way that is as empirical and model independent as possible. We collect and exploit these data in order to measure from the spectral energy distributions (SEDs) precisely how much stellar radiation is intercepted and re-radiated by dust, and how this quantity varies with galaxy properties. By including SPIRE data, we are more sensitive to emission from cold dust grains than previous analyses at shorter wavelengths, allowing for more accurate estimates of dust temperatures and masses. The dust/stellar flux ratio, which we measure by integrating the SEDs, has a range of nearly three decades (from 10(-2.2) to 10(0.5)). The inclusion of SPIRE data shows that estimates based on data not reaching these far-IR wavelengths are biased low by 17% on average. We find that the dust/stellar flux ratio varies with morphology and total infrared (IR) luminosity, with dwarf galaxies having faint luminosities, spirals having relatively high dust/stellar ratios and IR luminosities, and some early types having low dust/stellar ratios. We also find that dust/stellar flux ratios are related to gas-phase metallicity ((log(f(dust)/f(*)) over bar) = -0.66 +/- 0.08 and -0.22 +/- 0.12 for metal-poor and intermediate-metallicity galaxies, respectively), while the dust/stellar mass ratios are less so (differing by approximate to 0.2 dex); the more metal-rich galaxies span a much wider range of the flux ratios. In addition, the substantial scatter between dust/stellar flux and dust/stellar mass indicates that the former is a poor proxy of the latter. Comparing the dust/stellar flux ratios and dust temperatures, we also show that early types tend to have slightly warmer temperatures (by up to 5 K) than spiral galaxies, which may be due to more intense interstellar radiation fields, or possibly to different dust grain compositions. Finally, we show that early types and early-type spirals have a strong correlation between the dust/stellar flux ratio and specific star formation rate, which suggests that the relatively bright far-IR emission of some of these galaxies is due to ongoing (if limited) star formation as well as to the radiation field from older stars, which is heating the dust grains