45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

Research ArticleThe genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity±A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5' external transcribed spacer (5'-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5'-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5'-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5'-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5'-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.info:eu-repo/semantics/publishedVersio

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.publishersversionPeer reviewe

The Clustering of Galaxies in SDSS-III DR9 Baryon Oscillation Spectroscopic Survey: Constraints on Primordial Non-Gaussianity

We analyze the density field of 264,283 galaxies observed by the Sloan Digital Sky Survey (SDSS)-III Baryon Oscillation Spectroscopic Survey (BOSS) and included in the SDSS data release nine (DR9). In total, the SDSS DR9 BOSS data includes spectroscopic redshifts for over 400,000 galaxies spread over a footprint of more than 3,000 deg^2. We measure the power spectrum of these galaxies with redshifts 0.43 < z < 0.7 in order to constrain the amount of local non-Gaussianity, f_NL,local, in the primordial density field, paying particular attention to the impact of systematic uncertainties. The BOSS galaxy density field is systematically affected by the local stellar density and this influences the ability to accurately measure f_NL,local. In the absence of any correction, we find (erroneously) that the probability that f_NL,local is greater than zero, P(f_NL,local >0), is 99.5%. After quantifying and correcting for the systematic bias and including the added uncertainty, we find -45 < f_NL,local 0) = 91.0%. A more conservative approach assumes that we have only learned the k-dependence of the systematic bias and allows any amplitude for the systematic correction; we find that the systematic effect is not fully degenerate with that of f_NL,local, and we determine that -82 < f_NL,local < 178 (at 95% confidence) and P(f_NL,local >0) = 68%. This analysis demonstrates the importance of accounting for the impact of Galactic foregrounds on f_NL,local measurements. We outline the methods that account for these systematic biases and uncertainties. We expect our methods to yield robust constraints on f_NL,local for both our own and future large-scale-structure investigations.Comment: Matches version to be published in MNRAS. While in press, we found an error that caused all of our fNL values to be off by a factor of h^2. Our conclusions (and nearly 100% of the text) are unchanged because they were all in reference to the probability of fNL > 0 and the relative effect of systematics on the recovered constraint

Herbicide resistance-endowing ACCase gene mutations in hexaploid wild oat (Avena fatua): insights into resistance evolution in a hexaploid species

Many herbicide-resistant weed species are polyploids, but far too little about the evolution of resistance mutations in polyploids is understood. Hexaploid wild oat (Avena fatua) is a global crop weed and many populations have evolved herbicide resistance. We studied plastidic acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicide resistance in hexaploid wild oat and revealed that resistant individuals can express one, two or three different plastidic ACCase gene resistance mutations (Ile-1781-Leu, Asp-2078-Gly and Cys-2088-Arg). Using ACCase resistance mutations as molecular markers, combined with genetic, molecular and biochemical approaches, we found in individual resistant wild-oat plants that (1) up to three unlinked ACCase gene loci assort independently following Mendelian laws for disomic inheritance, (2) all three of these homoeologous ACCase genes were transcribed, with each able to carry its own mutation and (3) in a hexaploid background, each individual ACCase resistance mutation confers relatively low-level herbicide resistance, in contrast to high-level resistance conferred by the same mutations in unrelated diploid weed species of the Poaceae (grass) family. Low resistance conferred by individual ACCase resistance mutations is likely due to a dilution effect by susceptible ACCase expressed by homoeologs in hexaploid wild oat and/or differential expression of homoeologous ACCase gene copies. Thus, polyploidy in hexaploid wild oat may slow resistance evolution. Evidence of coexisting non-target-site resistance mechanisms among wild-oat populations was also revealed. In all, these results demonstrate that herbicide resistance and its evolution can be more complex in hexaploid wild oat than in unrelated diploid grass weeds. Our data provide a starting point for the daunting task of understanding resistance evolution in polyploids

Clustering analysis of high-redshift luminous red galaxies in Stripe 82

We present a clustering analysis of luminous red galaxies (LRGs) in Stripe 82 from the Sloan Digital Sky Survey (SDSS). We study the angular two-point autocorrelation function, w(θ), of a selected sample of over 130 000 LRG candidates via colour-cut selections in izK with the K-band coverage coming from UKIRT (United Kingdom Infrared Telescope) Infrared Deep Sky Survey (UKIDSS) Large Area Survey (LAS). We have used the cross-correlation technique of Newman to establish the redshift distribution of the LRGs. Cross-correlating them with SDSS quasi-stellar objects (QSOs), MegaZ-LRGs and DEEP Extragalactic Evolutionary Probe 2 (DEEP2) galaxies, implies an average redshift of the LRGs to be z ≈ 1 with space density, ng ≈ 3.20 ± 0.16 × 10−4 h3 Mpc−3. For θ ≤ 10 arcmin (corresponding to ≈10 h−1 Mpc), the LRG w(θ) significantly deviates from a conventional single power law as noted by previous clustering studies of highly biased and luminous galaxies. A double power law with a break at rb ≈ 2.4 h−1 Mpc fits the data better, with best-fitting scale length, r0, 1 = 7.63 ± 0.27 h−1 Mpc and slope γ1 = 2.01 ± 0.02 at small scales and r0, 2 = 9.92 ± 0.40 h−1 Mpc and γ2 = 1.64 ± 0.04 at large scales. Due to the flat slope at large scales, we find that a standard Λ cold dark matter (Λ CDM) linear model is accepted only at 2–3σ, with the best-fitting bias factor, b = 2.74 ± 0.07. We also fitted the halo occupation distribution (HOD) models to compare our measurements with the predictions of the dark matter clustering. The effective halo mass of Stripe 82 LRGs is estimated as Meff = 3.3 ± 0.6 × 1013 h−1 M⊙. But at large scales, the current HOD models did not help explain the power excess in the clustering signal. We then compare the w(θ) results to the results of Sawangwit et al. from three samples of photometrically selected LRGs at lower redshifts to measure clustering evolution. We find that a long-lived model may be a poorer fit than at lower redshifts, although this assumes that the Stripe 82 LRGs are luminosity-matched to the AAΩ LRGs. We find stronger evidence for evolution in the form of the z ≈ 1 LRG correlation function with the above flat two-halo slope maintaining to s ≳ 50 h− 1 Mpc. Applying the cross-correlation test of Ross et al., we find little evidence that the result is due to systematics. Otherwise, it may represent evidence for primordial non-Gaussianity in the density perturbations at early times, with flocalNL = 90 ± 30

Evolutionary insights inferred by molecular analysis of the ITS1-5.8S-ITS2 and IGS Avena sp. sequences

In an attempt to clarify phylogenetic and genome relationships among 35 diploid (A and C genomes), 13 tetraploid (AB and AC genomes) and 6 hexaploid (ACD genome) Avena taxa, 71 clones of the ITS1-5.8S-ITS2 fragment were sequenced, aligned and a network was constructed. In addition, the intergenic spacer (IGS) fragment was fingerprinted by means of a RFLP analysis using three different restriction enzymes. Both approaches led to comparable results. Clustering among the 54 Avena sp. entries was according to karyotype. Major genic divergence between the A and C genomes was revealed, while distinction among the A and B/D genomes was not possible. High affinity among the AB genome tetraploids and the A(s) genome diploid A. lusitanica was found, while AC genome tetraploids and ACD hexaploids were highly affiliated with the A(l) genome diploid A. longiglumis. The possible role of A. longiglumis in Avena sp. evolution is discussed

Evolution in the clustering strength of radio galaxies

We cross match the NVSS and FIRST surveys with three large photometric catalogues of luminous red galaxies (LRGs) to define radio-loud samples. These have median redshifts 0.35, 0.55 and 0.68 and, by matching rest-frame optical and radio properties, we construct uniform samples across the three surveys. This paper is concerned with the clustering properties of these samples derived from the angular correlation function. The primary aim is to characterise any evolution in the clustering amplitude of radio galaxies bellow z~0.68. We find no evidence for evolution in the large-scale (~1-50h^{-1}Mpc) clustering amplitude. Our radio galaxy autocorrelations are consistent with previous findings indicating little-to-no evolution in the redshift range 0.68 to 0 (~6Gyr of time). We also cross correlate radio galaxies with the parent LRG samples to increase the precision of our results and again find no evidence for evolution. Our results are inconsistent with a long-lived model for the clustering evolution that assumes radio sources randomly sample the LRG population. A model where the halo mass is constant with redshift is consistent with the data. This is similar to QSOs that have clustering amplitudes consistent with a single halo mass at all redshifts. Given that the brightest radio sources show stronger evolution in space density compared to fainter radio sources we restrict our samples to include only objects with L>10^{26}W/Hz and repeat the analysis. Again we find no evidence for evolution in the comoving correlation amplitude. These radio sources appear to inhabit the same mass halos as fainter radio galaxies (~9x10^{13}h^{-1}M_\odot). These halos are ~twice as massive as those of the general LRG population and ~30 times as massive as optical AGN/QSOs.Comment: 9 pages, 8 figures, accepted MNRA

[Treatment of the aortic valve and ascending aorta. The significance of reconstructive methods on the aortic root]

BACKGROUND AND OBJECTIVE: The standard surgical repair of disease of the aortic valve and the ascending aorta has been combined replacement, which includes the disadvantage of inserting a mechanical valve. We have investigated an individualized approach which preserves the native valve. PATIENTS AND METHODS: Between October 1995 and October 1997, a consecutive total of 101 patients (72 men, 29 women, aged 21-83 years) underwent operations for disease of the ascending aorta: aortic dissection type A in 34 patients, aneurysmal dilatation in 67. Dilatation of the aortic arch was associated with aortic regurgitation in 58 patients. There were 11 patients with aortic valve stenosis or previously implanted aortic valve prosthesis among a total of 46 whose aortic valve was replaced (group II). Supracommissural aortic replacement with a Dacron tube was performed in 16 patients (group I) with normal valve cusps and an aortic root diameter 5.0 cm (group IV). RESULTS: Operative intervention was electively performed in 72 patients, without any death. Of 29 patients operated as an emergency for acute type A dissection four died (14%). In 55 of the 58 patients with aortic regurgitation in proved possible to preserve native aortic valve (95%). In the early postoperative phase and after an average follow-up time of 11.8 months, transthoracic echocardiography demonstrated good aortic valve function, except in one patient each of groups III and IV who developed aortic regurgitation grades I or II. CONCLUSION: The described individualized approach makes it possible to preserve the native aortic valve in most patients with aortic regurgitation, at a low risk. Follow-up observations so far indicate good results of the reconstruction

The Role of Proteases in Determining Stomatal Development and Tuning Pore Aperture: A Review

Plant proteases, the proteolytic enzymes that catalyze protein breakdown and recycling, play an essential role in a variety of biological processes including stomatal development and distribution, as well as, systemic stress responses. In this review, we summarize what is known about the participation of proteases in both stomatal organogenesis and on the stomatal pore aperture tuning, with particular emphasis on their involvement in numerous signaling pathways triggered by abiotic and biotic stressors. There is a compelling body of evidence demonstrating that several proteases are directly or indirectly implicated in the process of stomatal development, affecting stomatal index, density, spacing, as well as, size. In addition, proteases are reported to be involved in a transient adjustment of stomatal aperture, thus orchestrating gas exchange. Consequently, the proteases-mediated regulation of stomatal movements considerably affects plants' ability to cope not only with abiotic stressors, but also to perceive and respond to biotic stimuli. Even though the determining role of proteases on stomatal development and functioning is just beginning to unfold, our understanding of the underlying processes and cellular mechanisms still remains far from being completed