Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome

Funded by: Leonardo da Vinci programme, Marie Curie programme, Natural Environment Research Council. Grant Number: NE/G01724/1, Czech Science Foundation. Grant Number: P501/13/10057S

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

17 p., tablas, gráficos.In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes ( T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.The work was supported by the Czech Science Foundation (P501/13/10057S and P501/12/G090) and NERC (UK).Peer reviewe

Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway

We are grateful for the FP7 Marie Curie IEF (Lu Ma), the FP7 Marie Curie ITN INTERCROSSING (Andrea Hatlen), the Czech Science Foundation (501/12/G090, Ales Kovarik), China Scholarship Council (Wencai Wang), and NERC (NE/ G01724/1, Laura Kelly, Ilia Leitch, Andrew Leitch). The Illumina sequencing of Fritillaria was funded by NERC (NE/G01724/1) and generated by the Centre of Genomic Research in the University of Liverpool, UK. This research utilised Queen Mary's MidPlus computational facilities, supported by QMUL Research-IT and funded by EPSRC grant EP/K000128/1. We thank an anonymous referee for a rigorous, insightful and helpful revie

Charmonium Suppression - Interplay of Hadronic and Partonic Degrees of Freedom

Last year the E866-group of the Fermilab measured the $x_F$ dependence of $J/\Psi$ and $\Psi'$ suppression in $pA$ collisions. We discuss two of the effects found in that experiment with regard to color coherence effects: the different suppression of the $J/\Psi$ and the $\Psi'$ at $x_F<0$ and the significant suppression of both at large $x_F$. The small $x_F$ regions is dominated by fully formed charmonium states and thus enables us to discuss the formation time and the cross section of the different charmonium states. In the large $x_F$ region the interaction of the charmonium states with nuclear matter has to be described by partonic degrees of freedom, because in that kinematic domain the formation time is much larger than the nuclear radii. The understanding of this region will be crucial for the interpretation of the data of the future heavy ion colliders RHIC and LHC.Comment: 4 pages, 1 table, 1 figure, Contribution to the Proceedings of the 15th Particles and Nuclei International Conference (PANIC 99), Uppsala, Sweden, June 10-16, 199

Cellular Scaling Rules of Insectivore Brains

Insectivores represent extremes in mammalian body size and brain size, retaining various “primitive” morphological characteristics, and some species of Insectivora are thought to share similarities with small-bodied ancestral eutherians. This raises the possibility that insectivore brains differ from other taxa, including rodents and primates, in cellular scaling properties. Here we examine the cellular scaling rules for insectivore brains and demonstrate that insectivore scaling rules overlap somewhat with those for rodents and primates such that the insectivore cortex shares scaling rules with rodents (increasing faster in size than in numbers of neurons), but the insectivore cerebellum shares scaling rules with primates (increasing isometrically). Brain structures pooled as “remaining areas” appear to scale similarly across all three mammalian orders with respect to numbers of neurons, and the numbers of non-neurons appear to scale similarly across all brain structures for all three orders. Therefore, common scaling rules exist, to different extents, between insectivore, rodent, and primate brain regions, and it is hypothesized that insectivores represent the common aspects of each order. The olfactory bulbs of insectivores, however, offer a noteworthy exception in that neuronal density increases linearly with increasing structure mass. This implies that the average neuronal cell size decreases with increasing olfactory bulb mass in order to accommodate greater neuronal density, and represents the first documentation of a brain structure gaining neurons at a greater rate than mass. This might allow insectivore brains to concentrate more neurons within the olfactory bulbs without a prohibitively large and metabolically costly increase in structure mass

Preoperative systemic inflammation predicts postoperative infectious complications in patients undergoing curative resection for colorectal cancer

The presence of systemic inflammation before surgery, as evidenced by the glasgow prognostic score (mGPS), predicts poor long-term survival in colorectal cancer. The aim was to examine the relationship between the preoperative mGPS and the development of postoperative complications in patients undergoing potentially curative resection for colorectal cancer. Patients (n=455) who underwent potentially curative resections between 2003 and 2007 were assessed consecutively, and details were recorded in a database. The majority of patients presented for elective surgery (85%) were over the age of 65 years (70%), were male (58%), were deprived (53%), and had TNM stage I/II disease (61%), had preoperative haemoglobin (56%), white cell count (87%) and mGPS 0 (58%) in the normal range. After surgery, 86 (19%) patients developed a postoperative complication; 70 (81%) of which were infectious complications. On multivariate analysis, peritoneal soiling (P&#60;0.01), elevated preoperative white cell count (P&#60;0.05) and mGPS (P&#60;0.01) were independently associated with increased risk of developing a postoperative infection. In elective patients, only the mGPS (OR=1.75, 95% CI=1.17-2.63, P=0.007) was significantly associated with increased risk of developing a postoperative infection. Preoperative elevated mGPS predicts increased postoperative infectious complications in patients undergoing potentially curative resection for colorectal cancer

Relationship between emergency presentation, systemic inflammatory response, and cancer-specific survival in patients undergoing potentially curative surgery for colon cancer

Background Emergency presentation is recognized to be associated with poorer cancer-specific survival following curative resection for colorectal cancer. The present study examined the hypothesis that an enhanced systemic inflammatory response, prior to surgery, might explain the impact of emergency presentation on survival. Methods In all, 188 patients undergoing potentially curative resection for colorectal cancer were studied. Of these, 55 (29&#37;) presented as emergencies. The systemic inflammatory response was assessed using the Glasgow Prognostic Score (mGPS), which is the combination of an elevated C-reactive protein (&gt;10 mg/L) and hypoalbuminemia (&lt;35 g/L). Results In the emergency group, tumor stage was greater (P &lt; 0.01), more patients received adjuvant therapy (P &lt; 0.01) more patients had an elevated mGPS (P &lt; 0.01), and more patients died of their disease (P &lt; 0.05). The minimum follow-up was 12 months; the median follow-up of the survivors was 48 months. Emergency presentation was associated with poorer 3-year cancer-specific survival in those patients aged 65 to 74 years (P &lt; 0.01), in both males and females (P &lt; 0.05), in the deprived (P &lt; 0.01), in patients with tumor-node-metastasis (TNM) stage II disease (P &lt; 0.01), in those who received no adjuvant therapy (P &lt; 0.01), and in the mGPS 0 and 1 groups (P &lt; 0.05) groups. On multivariate survival analysis of patients undergoing potentially curative surgery for TNM stage II colon cancer, emergency presentation (P &lt; 0.05) and mGPS (P &lt; 0.05) were independently associated with cancer-specific survival. Conclusions These results suggest that emergency presentation and the presence of systemic inflammatory response prior to surgery are linked and account for poorer cancer-specific survival in patients undergoing potentially curative surgery for colon cancer. Both emergency presentation and an elevated mGPS should be taken into account when assessing the likely outcome of these patients

Polarization Diffusion from Spacetime Uncertainty

A model of Lorentz invariant random fluctuations in photon polarization is presented. The effects are frequency dependent and affect the polarization of photons as they propagate through space. We test for this effect by confronting the model with the latest measurements of polarization of Cosmic Microwave Background (CMB) photons.Comment: 4 pages, 1 figur

Genomic repeat abundances contain phylogenetic signal

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution

An Anomalous Component of Galactic Emission

We present results from microwave background observations at the Owens Valley Radio Observatory. These observations, at 14.5 and 32 GHz, are designed to detect intrinsic anisotropy on scales of 7'. After point source removal, we detect significant emission with temperature spectral index beta ~ -2 towards the North Celestial Pole (NCP). Comparison of our data with the IRAS 100 micron map of the same fields reveals a strong correlation between this emission and the infrared dust emission. From the lack of detectable H-alpha emission, we conclude that the signals are consistent either with flat-spectrum synchrotron radiation, or with free-free emission from T_e ~ 10^6 K gas, probably associated with a large HI feature known as the NCP Loop. Assuming beta = -2.2, our data indicate a conversion T_f/I_(100 micron) = 0.075*nu(GHz)^-2.2 K/(MJy/sr). The detection of such a component suggests that we should be cautious in any assumptions made regarding foregrounds when designing experiments to map the microwave background radiation.Comment: 6 pages, Latex, 3 Postscript figures, uses aas2pp4.st