Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth

<p>Abstract</p> <p>Background</p> <p>The roles of non-coding RNAs in regulating gene expression have been extensively studied in both prokaryotes and eukaryotes, however few reports exist as to their roles in organellar gene regulation. Evidence for accumulation of natural antisense RNAs (asRNAs) in chloroplasts comes from the expressed sequence tag database and cDNA libraries, while functional data have been largely obtained from artificial asRNAs. In this study, we used <it>Nicotiana tabacum </it>to investigate the effect on sense strand transcripts of overexpressing a natural chloroplast asRNA, AS5, which is complementary to the region which encodes the 5S rRNA and tRNA^Arg.</p> <p>Results</p> <p>AS5-overexpressing (AS5^ox) plants obtained by chloroplast transformation exhibited slower growth and slightly pale green leaves. Analysis of AS5 transcripts revealed four distinct species in wild-type (WT) and AS5^oxplants, and additional AS5^ox-specific products. Of the corresponding sense strand transcripts, tRNA^Argoveraccumulated several-fold in transgenic plants whereas 5S rRNA was unaffected. However, run-on transcription showed that the 5S-<it>trnR </it>region was transcribed four-fold more in the AS5^oxplants compared to WT, indicating that overexpression of AS5 was associated with decreased stability of 5S rRNA. In addition, polysome analysis of the transformants showed less 5S rRNA and <it>rbcL </it>mRNA associated with ribosomes.</p> <p>Conclusions</p> <p>Our results suggest that AS5 can modulate 5S rRNA levels, giving it the potential to affect Chloroplast translation and plant growth. More globally, overexpression of asRNAs via chloroplast transformation may be a useful strategy for defining their functions.</p

kt Effects in Direct-Photon Production

We discuss the phenomenology of initial-state parton-kt broadening in direct-photon production and related processes in hadron collisions. After a brief summary of the theoretical basis for a Gaussian-smearing approach, we present a systematic study of recent results on fixed-target and collider direct-photon production, using complementary data on diphoton and pion production to provide empirical guidance on the required amount of kt broadening. This approach provides a consistent description of the observed pattern of deviation of next-to-leading order QCD calculations relative to the direct-photon data, and accounts for the shape and normalization difference between fixed-order perturbative calculations and the data. We also discuss the uncertainties in this phenomenological approach, the implications of these results on the extraction of the gluon distribution of the nucleon, and the comparison of our findings to recent related work.Comment: LaTeX, uses revtex and epsf, 37 pages, 15 figure

Generic User Process Interface for Event Generators

Generic Fortran common blocks are presented for use by High Energy Physics event generators for the transfer of event configurations from parton level generators to showering and hadronization event generators.Comment: Physics at TeV Colliders II Workshop, Les Houches, France, May 2001 14 pages, 6 figure

The impact of new neutrino DIS and Drell-Yan data on large-x parton distributions

New data sets have recently become available for neutrino and antineutrino deep inelastic scattering on nuclear targets and for inclusive dimuon production in pp pd interactions. These data sets are sensitive to different combinations of parton distribution functions in the large-x region and, therefore, provide different constraints when incorporated into global parton distribution function fits. We compare and contrast the effects of these new data on parton distribution fits, with special emphasis on the effects at large x. The effects of the use of nuclear targets in the neutrino and antineutrino data sets are also investigated.Comment: 24 pages, 13 figure

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent

© 2015 Roulis et al. Background: The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results: In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions: Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates

Examination of direct-photon and pion production in proton-nucleon collisions

We present a study of inclusive direct-photon and pion production in hadronic interactions, focusing on a comparison of the ratio of gamma/pi0 yields with expectations from next-to-leading order perturbative QCD (NLO pQCD). We also examine the impact of a phenomenological model involving k_T smearing (which approximates effects of additional soft-gluon emission) on absolute predictions for photon and pion production and their ratio.Comment: 20 pages, 12 figures. Minor changes in wording and in figure

Huddle test measurement of a near Johnson noise limited geophone

In this paper, the sensor noise of two geophone configurations (L-22D and L-4C geophones from Sercel with custom built amplifiers) was measured by performing two huddle tests. It is shown that the accuracy of the results can be significantly improved by performing the huddle test in a seismically quiet environment and by using a large number of reference sensors to remove the seismic foreground signal from the data. Using these two techniques, the measured sensor noise of the two geophone configurations matched the calculated predictions remarkably well in the bandwidth of interest (0.01 Hz–100 Hz). Low noise operational amplifiers OPA188 were utilized to amplify the L-4C geophone to give a sensor that was characterized to be near Johnson noise limited in the bandwidth of interest with a noise value of 10−11 m/Hz⎯⎯⎯⎯⎯√10−11 m/Hz at 1 Hz

Koala cathelicidin PhciCath5 has antimicrobial activity, including against Chlamydia pecorum.

Devastating fires in Australia over 2019-20 decimated native fauna and flora, including koalas. The resulting population bottleneck, combined with significant loss of habitat, increases the vulnerability of remaining koala populations to threats which include disease. Chlamydia is one disease which causes significant morbidity and mortality in koalas. The predominant pathogenic species, Chlamydia pecorum, causes severe ocular, urogenital and reproductive tract disease. In marsupials, including the koala, gene expansions of an antimicrobial peptide family known as cathelicidins have enabled protection of immunologically naïve pouch young during early development. We propose that koala cathelicidins are active against Chlamydia and other bacteria and fungi. Here we describe ten koala cathelicidins, five of which contained full length coding sequences that were widely expressed in tissues throughout the body. Focusing on these five, we investigate their antimicrobial activity against two koala C. pecorum isolates from distinct serovars; MarsBar and IPTaLE, as well as other bacteria and fungi. One cathelicidin, PhciCath5, inactivated C. pecorum IPTaLE and MarsBar elementary bodies and significantly reduced the number of inclusions compared to the control (p<0.0001). Despite evidence of cathelicidin expression within tissues known to be infected by Chlamydia, natural PhciCath5 concentrations may be inadequate in vivo to prevent or control C. pecorum infections in koalas. PhciCath5 also displayed antimicrobial activity against fungi and Gram negative and positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Electrostatic interactions likely drive PhciCath5 adherence to the pathogen cell membrane, followed by membrane permeabilisation leading to cell death. Activity against E. coli was reduced in the presence of 10% serum and 20% whole blood. Future modification of the PhciCath5 peptide to enhance activity, including in the presence of serum/blood, may provide a novel solution to Chlamydia infection in koalas and other species

Les Houches Guidebook to Monte Carlo Generators for Hadron Collider Physics

Recently the collider physics community has seen significant advances in the formalisms and implementations of event generators. This review is a primer of the methods commonly used for the simulation of high energy physics events at particle colliders. We provide brief descriptions, references, and links to the specific computer codes which implement the methods. The aim is to provide an overview of the available tools, allowing the reader to ascertain which tool is best for a particular application, but also making clear the limitations of each tool.Comment: 49 pages Latex. Compiled by the Working Group on Quantum ChromoDynamics and the Standard Model for the Workshop ``Physics at TeV Colliders'', Les Houches, France, May 2003. To appear in the proceeding