Generalized embedding variables for geometrodynamics and spacetime diffeomorphisms: Ultralocal coordinate conditions

We investigate the embedding variable approach to geometrodynamics advocated in work by Isham, Kucha\v{r} and Unruh for a general class of coordinate conditions that mirror the Isham-Kucha\v{r} Gaussian condition but allow for arbitrary algebraic complexity. We find that the same essential structure present in the ultralocal Gaussian condition is repeated in the general case. The resultant embedding--extended phase space contains a full representation of the Lie algebra of the spacetime diffeomorphism group as well as a consistent pure gravity sector.Comment: 16 page

A Kucha\v{r} Hypertime Formalism For Cylindrically Symmetric Spacetimes With Interacting Scalar Fields

The Kucha\v{r} canonical transformation for vacuum geometrodynamics in the presence of cylindrical symmetry is applied to a general non-vacuum case. The resulting constraints are highly non-linear and non-local in the momenta conjugate to the Kucha\v{r} embedding variables. However, it is demonstrated that the constraints can be solved for these momenta and thus the dynamics of cylindrically symmetric models can be cast in a form suitable for the construction of a hypertime functional Schr\"odinger equation.Comment: 5 pages, LaTeX, UBCTP-93-02

To the North Coast of Devon: Collaborative Navigation While Exploring Unfamiliar Terrain

Navigation-knowing where one is and finding a safe route-is a fundamental aspect of all exploration. In unfamiliar terrain, one may use maps and instruments such as a compass or binoculars to assist, and people often collaborate in finding their way. This paper analyzes a group of people driving a humvee from a base camp to the north coast of Devon Island in the High Canadian Arctic. A complete audio recording and video during most stops allows a quantitative and semantic analysis of the conversations when the team stopped to take bearings and replan a route. Over a period of 2 hours, the humvee stopped 20 times, with an average duration of 3.15 min/pause and 3.85 min moving forward. The team failed to reach its goal due to difficult terrain causing mechanical problems. The analysis attempts to explain these facts by considering a variety of complicating factors, especially the navigation problem of relating maps and the world to locate the humvee and to plan a route. The analysis reveals patterns in topic structure and turn-taking, supporting the view that the collaboration was efficient, but the tools and information were inadequate for the task. This work is relevant for planning and training for planetary surface missions, as well as developing computer systems that could aid navigation

Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth

<p>Abstract</p> <p>Background</p> <p>The ascomycete fungus <it>Cercospora zeae-maydis </it>is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in <it>C. zeae-maydis </it>at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs) from <it>C. zeae-maydis </it>and evaluate their expression during vegetative, infectious, and reproductive growth.</p> <p>Results</p> <p>A total of 27,551 ESTs was obtained from five cDNA libraries constructed from vegetative and sporulating cultures of <it>C. zeae-maydis</it>. The ESTs, grouped into 4088 clusters and 531 singlets, represented 4619 putative unique genes. Of these, 36% encoded proteins similar (E value ≤ 10^-05) to characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions and biological processes based on Gene Ontology (GO) classification. We identified numerous, previously undescribed genes with potential roles in photoreception, pathogenesis, and the regulation of development as well as <it>Zephyr</it>, a novel, actively transcribed transposable element. Differential expression of selected genes was demonstrated by real-time PCR, supporting their proposed roles in vegetative, infectious, and reproductive growth.</p> <p>Conclusion</p> <p>Novel genes that are potentially involved in regulating growth, development, and pathogenesis were identified in <it>C. zeae-maydis</it>, providing specific targets for characterization by molecular genetics and functional genomics. The EST data establish a foundation for future studies in evolutionary and comparative genomics among species of <it>Cercospora </it>and other groups of plant pathogenic fungi.</p

Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth

<p>Abstract</p> <p>Background</p> <p>The ascomycete fungus <it>Cercospora zeae-maydis </it>is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in <it>C. zeae-maydis </it>at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs) from <it>C. zeae-maydis </it>and evaluate their expression during vegetative, infectious, and reproductive growth.</p> <p>Results</p> <p>A total of 27,551 ESTs was obtained from five cDNA libraries constructed from vegetative and sporulating cultures of <it>C. zeae-maydis</it>. The ESTs, grouped into 4088 clusters and 531 singlets, represented 4619 putative unique genes. Of these, 36% encoded proteins similar (E value ≤ 10^-05) to characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions and biological processes based on Gene Ontology (GO) classification. We identified numerous, previously undescribed genes with potential roles in photoreception, pathogenesis, and the regulation of development as well as <it>Zephyr</it>, a novel, actively transcribed transposable element. Differential expression of selected genes was demonstrated by real-time PCR, supporting their proposed roles in vegetative, infectious, and reproductive growth.</p> <p>Conclusion</p> <p>Novel genes that are potentially involved in regulating growth, development, and pathogenesis were identified in <it>C. zeae-maydis</it>, providing specific targets for characterization by molecular genetics and functional genomics. The EST data establish a foundation for future studies in evolutionary and comparative genomics among species of <it>Cercospora </it>and other groups of plant pathogenic fungi.</p

Actes du Symposium International - Le livre, la Roumanie, l’Europe / Proceedings of the International Symposium Books, Romania, Europe - 5ème édition 24-26 septembre 2012

Tome 2 des actes du Symposium International "Le livre, la Roumanie, L\u27Europe" qui s\u27est tenu les 24, 25 et 26 septembre 2012 à Mamaia, Roumanie, organisé par la Bibliothèque Métropolitaine de Bucarest. / Tome 2 of the Proceedings of the International Symposium "Books, Romania, Europe" held on 24, 25 and 26 September 2012 in Mamaia, Romania, organized by the Bucharest Metropolitan Library. Textes réunis et présentés par : Réjean Savard Chantal Stanescu Hermina G.B. Anghelescu Cristina Io

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry.

We sequenced and compared the genomes of the Dothideomycete fungal plant pathogensCladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu \u3e61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicolawas sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed “mesosynteny” is very different from synteny seen between other organisms. A surprising feature of the M. graminicolagenome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins ( HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.This is the publisher’s final pdf. The published article is copyrighted by The Genetics Society of America and can be found at: http://www.genetics-gsa.org/Keywords: ToxB, Anastomosis, Wheat (Triticum aestivum), Copy number variation, ToxA, Histone H3 transduplicationKeywords: ToxB, Anastomosis, Wheat (Triticum aestivum), Copy number variation, ToxA, Histone H3 transduplicatio

Appunti sul movimento antifascista sloveno della Venezia Giulia

<div><p>The class <em>Dothideomycetes</em> is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The <em>Dothideomycetes</em> most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several <em>Dothideomycetes</em> contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 <em>Dothideomycetes</em> offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the <em>Dothideomycetes</em>, the <em>Capnodiales</em> and <em>Pleosporales</em>, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most <em>Dothideomycetes</em> and upregulated during infection in <em>L. maculans</em>, suggesting a possible function in response to oxidative stress.</p> </div