The poetical works of Geoff. Chaucer...

Mode of access: Internet.

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus

We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility ( het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer ( HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated ""gene dumps'' and, perhaps, simultaneously, as "" gene factories''.

The 2008 update of the Aspergillus nidulans genome annotation: A community effort

The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.

A method to lower the detection limit for optical beat signals from a frequency-dithered stabilized laser

A narrow absorption feature in an atomic or molecular gas (such as iodine or methane) is used as the frequency reference in many stabilized lasers. As part of the stabilization scheme an optical frequency dither is applied to the laser. In optical heterodyne experiments, this dither is transferred to the RF beat signal, reducing the spectral power density and hence the signal to noise ratio over that in the absence of dither. We removed the dither by mixing the raw beat signal with a dithered local oscillator signal. When the dither waveform is matched to that of the reference laser the output signal from the mixer is rendered dither free. Application of this method to a Winters iodine-stabilized helium-neon laser reduced the bandwidth of the beat signal from 6 MHz to 390 kHz, thereby lowering the detection threshold from 5 pW of laser power to 3 pW. In addition, a simple signal detection model is developed which predicts similar threshold reductions.

Spatial, temporal, and human dimensions of air pollution in Brisbane

Arriving in Brisbane some six years ago, I could not help being impressed by what may be prosaically described as its atmospheric amenity resources. Perhaps this in part was due to my recent experiences in major urban centres in North America, but since that time, that sparkling quality and the blue skies seem to have progressively diminished. Unfortunately, there is also objective evidence available to suggest that this apparent deterioration is not merely the result of habituation of the senses. Air pollution data for the city show trends of increasing concentrations of those very substances that have destroyed the attractiveness of major population centres elsewhere, with climates initially as salubrious. Indeed, present figures indicate that photochemical smog in unacceptably high concentrations is rapidly becoming endemic also over Brisbane. These regrettable developments should come as no surprise. The society at large has not been inclined to respond purposefully to warnings of impending environmental problems, despite the experiences and publicity from overseas and even from other cities within Australia. Nor, up to the present, have certain politicians and government officials displayed stances beyond those necessary for the maintenance of a decorum of concern. At this stage, there still exists the possibility for meaningful government action without the embarrassment of losing political favour with the electorate. To the contrary, there is every chance that such action may be turned to advantage with increased public enlightenment. It would be more than a pity to miss perhaps the final remaining opportunity: Queensland is one of the few remaining places in the world with sufficient resources to permit both rational development and high environmental quality. The choice appears to be one of making a relatively minor investment now for a large financial and social gain the near future, or, permitting Brisbane to degenerate gradually into just another stagnated Los Angeles or Sydney. The present monograph attempts to introduce the problem by reviewing the available research on air quality in the Brisbane area. It also tries to elucidate some seemingly obvious, but so far unapplied management approaches. By necessity, such a broad treatment needs to make inroads into extensive ranges of subject areas, including political and legal practices to public perceptions, scientific measurement and statistical analysis to dynamics of air flow. Clearly, it does not pretend to be definitive in any of these fields, but it does try to emphasize those adjustable facets of the human use system of natural resources, too often neglected in favour of air pollution control technology. The crossing of disciplinary boundaries, however, needs no apology: air quality problems are ubiquitous, touching upon space, time and human interaction.

Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA - Crystal structure of an oligomeric complex of yeast SmF

Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.

Quantum process tomography of a controlled-NOT gate

We demonstrate complete characterization of a two-qubit entangling process-a linear optics controlled-NOT gate operating with coincident detection-by quantum process tomography. We use a maximum-likelihood estimation to convert the experimental data into a physical process matrix. The process matrix allows an accurate prediction of the operation of the gate for arbitrary input states and a calculation of gate performance measures such as the average gate fidelity, average purity, and entangling capability of our gate, which are 0.90, 0.83, and 0.73, respectively.

International Society for Sexual Medicine`s Guidelines for the Diagnosis and Treatment of Premature Ejaculation

Introduction. Over the past 20 years our knowledge of premature ejaculation (PE) has significantly advanced. Specifically, we have witnessed substantial progress in understanding the physiology of ejaculation, clarifying the real prevalence of PE in population-based studies, reconceptualizing the definition and diagnostic criterion of the disorder, assessing the psychosocial impact on patients and partners, designing validated diagnostic and outcome measures, proposing new pharmacologic strategies and examining the efficacy, safety and satisfaction of these new and established therapies. Given the abundance of high level research it seemed like an opportune time for the International Society for Sexual Medicine (ISSM) to promulgate an evidenced-based, comprehensive and practical set of clinical guidelines for the diagnosis and treatment of PE. Aim. Develop clearly worded, practical, evidenced-based recommendations for the diagnosis and treatment of PE for family practice clinicians as well as sexual medicine experts. Method. Review of the literature. Results. This article contains the report of the ISSM PE Guidelines Committee. It affirms the ISSM definition of PE and suggests that the prevalence is considerably lower than previously thought. Evidence-based data regarding biological and psychological etiology of PE are presented, as is population-based statistics on normal ejaculatory latency. Brief assessment procedures are delineated and validated diagnostic and treatment questionnaires are reviewed. Finally, the best practices treatment recommendations are presented to guide clinicians, both familiar and unfamiliar with PE, in facilitating treatment of their patients. Conclusion. Development of guidelines is an evolutionary process that continually reviews data and incorporates the best new research. We expect that ongoing research will lead to a more complete understanding of the pathophysiology as well as new efficacious and safe treatments for this sexual dysfunction. Therefore, it is strongly recommended that these guidelines be re-evaluated and updated by the ISSM every 4 years. Althof SE, Abdo CHN, Dean J, Hackett G, McCabe M, McMahon CG, Rosen RC, Sadovsky R, Waldinger M, Becher E, Broderick GA, Buvat J, Goldstein I, El-Meliegy AI, Giuliano F, Hellstrom WJG, Incrocci L, Jannini EA, Park K, Parish S, Porst H, Rowland D, Segraves R, Sharlip I, Simonelli C, and Tan HM. International Society for Sexual Medicine`s guidelines for the diagnosis and treatment of premature ejaculation. J Sex Med 2010;7:2947-2969.