The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments

RNA editing alters plant mitochondrial and chloroplast transcripts by converting specific cytidines to uridines, which usually results in a change in the amino acid sequence of the translated protein. Systematic studies have experimentally identified sites of RNA editing in organellar transcriptomes from several species, but these analyses have not kept pace with rate of genome sequencing. The PREP (predictive RNA editors for plants) suite was developed to computationally predict sites of RNA editing based on the well-known principle that editing in plant organelles increases the conservation of proteins across species. The PREP suite provides predictive RNA editors for plant mitochondrial genes (PREP-Mt), for chloroplast genes (PREP-Cp), and for alignments submitted by the user (PREP-Aln). These servers require minimal input, are very fast, and are highly accurate on all seed plants examined to date. PREP-Mt has proved useful in several research studies and the newly developed PREP-Cp and PREP-Aln servers should be of further assistance for analyses that require knowledge of the location of sites of RNA editing. The PREP suite is freely available at http://prep.unl.edu/

Cavity-enabled high-dimensional quantum key distribution

High-dimensional quantum key distribution (QKD) offers the possibility of encoding multiple bits of key on a single entangled photon pair. An experimentally promising approach to realizing this is to use energy–time entanglement. Currently, however, the control of very high-dimensional entangled photons is challenging. We present a simple and experimentally compact approach, which is based on a cavity that allows one to measure two different bases: the time of arrival and another that is approximately mutually unbiased to the arrival time. We quantify the errors in the setup, due both to the approximate nature of the mutually unbiased measurement and as a result of experimental errors. It is shown that the protocol can be adapted using a cut-off so that it is robust against the considered errors, even within the regime of up to 10 bits per photon pair

Microwave Gaseous Discharges

Contains reports on five research projects.United States Atomic Energy Commission (Contract AT (30-1) 1842

D'yakonov-Perel' spin relaxation for degenerate electrons in the electron-hole liquid

We present an analytical study of the D'yakonov-Perel' spin relaxation time for degenerate electrons in a photo-excited electron-hole liquid in intrinsic semiconductors exhibiting a spin-split band structure. The D'yakonov-Perel' spin relaxation of electrons in these materials is controlled by electron-hole scattering, with small corrections from electron-electron scattering and virtually none from electron-impurity scattering. We derive simple expressions (one-dimensional and two-dimensional integrals respectively) for the effective electron-hole and electron-electron scattering rates which enter the spin relaxation time calculation. The electron-hole scattering rate is found to be comparable to the scattering rates from impurities in the electron liquid - a common model for n-type doped semiconductors. As the density of electron-hole pairs decreases (within the degenerate regime), a strong enhancement of the scattering rates and a corresponding slowing down of spin relaxation is predicted due to exchange and correlation effects in the electron-hole liquid. In the opposite limit of high density, the original D'yakonov-Perel' model fails due to decreasing scattering rates and is eventually superseded by free precession of individual quasiparticle spins.Comment: 16 pages, 5 figure

Assessing Anthocyanin Biosynthesis in Solanaceae as a Model Pathway for Secondary Metabolism

Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI annotation pipeline generated more and longer FBP annotations on average than genome-specific annotation pipelines. The pattern of diversification of each enzyme among asterids was assessed by phylogenetic analysis, showing that the CHS superfamily encompasses a large paralogous family of ancient and recent duplicates, whereas other FBP enzymes have diversified via recent duplications in particular lineages. Heterologous expression of a pansy F3050H gene in tobacco changed flower color from pink to dark purple, demonstrating that anthocyanin production can be predictably modified using reverse genetics. These results suggest that the Solanaceae FBP could be an ideal system to model genotype-to-phenotype interactions for secondary metabolism

Neurocysticercosis in Radiographically Imaged Seizure Patients in U.S. Emergency Departments1

Neurocysticercosis appears to be on the rise in the United States, based on immigration patterns and published cases series, including reports of domestic acquisition. We used a collaborative network of U.S. emergency departments to characterize the epidemiology of neurocysticercosis in seizure patients. Data were collected prospectively at 11 university-affiliated, geographically diverse, urban U.S. emergency departments from July 1996 to September 1998. Patients with a seizure who underwent neuroimaging were included. Of the 1,801 patients enrolled in the study, 38 (2.1%) had seizures attributable to neurocysticercosis. The disease was detected in 9 of the 11 sites and was associated with Hispanic ethnicity, immigrant status, and exposure to areas where neurocysticercosis is endemic. This disease appears to be widely distributed and highly prevalent in certain populations (e.g., Hispanic patients) and areas (e.g., Southwest)

Association Between Appendectomy and Clostridium difficile Infection

BackgroundRecent theory proposes that the appendix functions as a reservoir for commensal bacteria, and serves to re-inoculate the colon with normal flora in the event of pathogen exposure or purging of intestinal flora. If true, we reasoned that flora from a normal appendix could provide protection against Clostridium difficile. We conducted this investigation to examine the protective effect of an intact appendix and test the hypothesis that prior appendectomy will be more common among patients with a positive test for C. difficile as compared with patients who test negative.MethodsWe contacted patients who had undergone C. difficile testing and asked them whether or not they had a prior appendectomy. Using their responses and results from Toxin A & B EIA tests, we calculated the difference in appendectomy rates between those who tested positive for C. difficile, and those who tested negative. We considered a positive 15% absolute difference to represent a significant increase in appendectomy rate.ResultsWe enrolled 257 patients. Among the 136 who tested positive for C. difficile, 27 (19.9%) had prior appendectomies, while among 121 patients testing negative for C. difficile, 38 (31.4%) had prior appendectomies, yielding a difference in appendectomy rates of -11.6% (95% Confidence Interval: -21.6% to -0.9%).ConclusionsThe rate of prior appendectomy was actually lower among patients with a positive C. difficile test as compared to those with a negative test. Conversely, patients who tested positive for C. difficile were more likely to have an intact appendix than those who tested negative. These results suggest that rather than being protective, an intact appendix appears to promote C. difficile acquisition, carriage, and disease.KeywordsClostridium difficile; Appendix; Appendectomy; Microbial reservoir; Infection

Microwave Gaseous Disharges

Contains reports on seven research projects.Atomic Energy Commission under Contract AT(30-1)184