Aspects of Large Scale Symbolic Computation Management

The special-purpose computer algebra system FELIX is designed for computations in constructive commutative and non-commutative algebra. In this paper we discuss some features of the system supporting the computation of rather complex problems, especially standard basis computations, using standard hardware. There is a frst aspect concerning the definition and implementation of the basic data types which should be a good compromise between space and time efficient representations of the algebraic objects. Usually, rather complex computations are very time consuming (up to weeks) and often require several attempts. So, there are included special session saving methods in FELIX which allows to backup the attained intermediate results in form of memory images into special session files and to restart later on. Finally, we describe our efforts crunching complex problems by parallelization. The implemented interface is based on stream sockets and includes a special protocol for the data exchange. It supports the distributed computation on heterogeneous, loosely coupled systems

Characterization of the Snowy Cotyledon 1 Mutant of Arabidopsis Thaliana: The Impact of Chloroplast Elongation Factor G on Chloroplast Development and Plant Vitality

During seedling development chloroplast formation marks the transition from heterotrophic to autotrophic growth. The development and activity of chloroplasts may differ in cotyledons that initially serve as a storage organ and true leaves whose primary function is photosynthesis. A genetic screen was used for the identification of genes that affect selectively chloroplast function in cotyledons of Arabidopsis thaliana. Several mutants exhibiting pale cotyledons and green true leaves were isolated and dubbed snowy cotyledon (sco).One of the mutants, sco1, was characterized in more detail. The mutated gene was identified using map-based cloning. The mutant contains a point mutation in a gene encoding the chloroplast elongation factor G, leading to an amino acid exchange within the predicted 70S ribosome-binding domain. The mutation results in a delay in the onset of germination. At this early developmental stage embryos still contain undifferentiated proplastids, whose proper function seems necessary for seed germination. In light-grown sco1 seedlings the greening of cotyledons is severely impaired, whereas the following true leaves develop normally as in wild-type plants. Despite this apparent similarity of chloroplast development in true leaves of mutant and wild-type plants various aspects of mature plant development are also affected by the sco1 mutation such as the onset of flowering, the growth rate, and seed production. The onset of senescence in the mutant and the wild-type plants occurs, however, at the same time, suggesting that in the mutant this particular developmental step does not seem to suffer from reduced protein translation efficiency in chloroplast

A genetic approach towards elucidating the biological activity of different reactive oxygen species in Arabidopsis thaliana

Plants are often exposed to external conditions that adversely affect their growth, development or productivity. Such unfavourable environmental stress factors may result in rapid and transient increases of intracellular concentrations of reactive oxygen species (ROS) that are chemically distinct and impact plants either by being cytotoxic or by acting as a signal. Because different ROS are generated simultaneously in different cellular and extracellular compartments, it is almost impossible to link a particular ROS to a specific stress response and to determine its mode of action. The conditional flu mutant of Arabidopsis has been used to determine the biological role of singlet oxygen. Immediately after a dark/light shift of the flu mutant, singlet oxygen is generated within the plastids activating several stress responses that include growth inhibition of mature plants and seedling lethality. These stress responses do not result from physicochemical damage caused by singlet oxygen, but are attributable to the activation of a genetically determined stress response programme triggered by the Executer1 protein. Singlet oxygen-mediated stress responses at the transcriptional level necessitate a retrograde transduction of signals from the chloroplast to the nucleus that activate distinct sets of genes different from those that are induced by superoxide/hydrogen peroxide. Hence, the biological activities of these two types of ROS are distinct from each other. Whether they act independently or interact is not known yet and is the topic of our current researc

The Atger3 promoter confers circadian clock-regulated transcription with peak expression at the beginning of the night

In Arabidopsis thaliana, steady-state abundance of the Atger3 transcript encoding a germin-like cell wall protein follows a circadian rhythm, reaching its highest level at the beginning of the night. As a first step towards dissecting the molecular mechanisms underlying these transcript oscillations, the Atger3 genomic locus was characterised. Transcriptional fusions of 1.8kb and 967bp Atger3 promoter fragments to the β-glucuronidase (GUS) reporter gene mediate high-amplitude circadian oscillations of the GUS transcript in transgenic Arabidopsis. 5′ deletion to −490 greatly reduces overall transcript abundance while retaining a basal oscillation. Further deletion to −299 abolishes preferential GUS expression in the evening. Taken together, these data indicate that clock-response elements contributing to high-amplitude Atger3 oscillations largely reside between −299 and −967. Histochemical staining for GUS activity indicates that the Atger3 promoter is active in cotyledons, young leaves, petioles, the inflorescence axis, pedicels, sepals, ovary, style and siliques but not in roots, petals and anther

Snowy cotyledon 2: the identification of a zinc finger domain protein essential for chloroplast development in cotyledons but not in true leaves

In cotyledons of etiolated seedlings light-dependent transformation of etioplasts to chloroplasts marks the transition from heterotrophic to autotrophic growth. Genetic factors required for this developmental step were identified by isolating mutants of Arabidopsis thaliana that were impaired in chloroplast development in cotyledons but not in true leaves. Several mutants with chlorophyll-deficient cotyledons were isolated and dubbed snowy cotyledon (sco). Here we describe the identification and detailed characterization of the snowy cotyledon 2 mutant. The mutated SCO2 gene was identified using a map-based cloning strategy. SCO2 was shown to encode a novel protein which contains a single DnaJ-like zinc finger domain. The SCO2 protein fused to GFP was shown to be present in chloroplasts. Inactivation of SCO2 has almost no detectable impact on the levels of transcripts encoding plastid-specific proteins but leads to a significant reduction of plastid protein levels. Even though transcripts of SCO2 have been found ubiquitously in green tissues as well as in roots phenotypic changes due to SCO2 inactivation are confined to cotyledons. The cotyledons in embryos of sco2 are unaffected in their chloroplast biogenesis. Upon precocious germination seedlings of sco2 and wild type are indistinguishable. The SCO2 mutation affects chloroplast biogenesis only at the end of dormancy during seed germination. The transition from heterotrophic to autotrophic growth is dramatically impaired in sco2 when seedlings were kept in the dark for more than 5days prior to light exposur

Lymphatische Mikrogefäßdichte in benignen und malignen Läsionen der Mamma: quantitative immunhistochemische Analyse der Antikörper D2-40 und LYVE-1 mit einer Untersuchung der Korrelation zur synchronen nodalen Metastasierung

In Industriestaaten ist das Mammakarzinom das häufigste Karzinom der weiblichen Bevölkerung, verschiedene Faktoren haben einen Einfluss auf den Verlauf und das Überleben bei dieser Erkrankung, eine besondere Bedeutung kommt der Angioneogenese zu. In der vorliegenden Arbeit soll unter Adaptation des von Weidner angewendeten Verfahrens zur Messung der Gefäßdichte in Tumoren die Lymphgefäßdichte in Läsionen der Mamma bestimmt werden und ob diese eine erhöhte Rate an axillären Lymphknotenmetastasen nach sich zieht, zwei immunhistochemische Marker sind zur Darstellung von lymphoendothelialen Strukturen verfügbar, die Antikörper LYVE-1 und D2-40 sind vergleichend im Brustgewebe zum Einsatz gekommen. Gewebsmaterial von 102 Patienten mit benignen und malignen Läsionen im Bereich der Mamma wurden in die Untersuchung einbezogen, bei der mikroskopischen Betrachtung zeigten sich auch Kreuzreaktionen der Antikörper gegen nicht lymphatische Strukturen, nach der vergleichenden Analyse erscheint D2-40 für Mammagewebe besser geeignet zu sein als LYVE-1, bei der statistischen Auswertung konnte der Nachweis erbracht werden, dass im Falle von axillären Lympknotenmetastasen eine Erhöhung der Lymphgefäßzahl im Tumor besteht, dies war insbesondere mit Hilfe von D2-40 beweisbar. Die lymphatische Mikrogefäßdichte ist als unabhängig von anderen Prognosefaktoren anzusehen, in die Untersuchung mit einbezogen wurde ein auf ein Fibroadenom beschränktes Karzinom, wie auch bei den anderen untersuchten Fibroadenomen konnten hier keine Lymphgefäße im Tumor gefunden werden, daraus ergibt sich der Ansatz, der zumindest deutlich eingeschränkten Kompetenz dieser Tumorentität zur lymphatischen Metastasierung. Die Untersuchung bestätigt den direkten Zusammenhang zwischen der erhöhten Lymphgefäßdichte und einer nodalen Metastasierung, offensichtlich bestehen jedoch konzeptionelle Unterschiede zwischen der Hämangio- und der Lymphangioneogenese

Arabidopsis mutants reveal multiple singlet oxygen signaling pathways involved in stress response and development

Shortly after the release of singlet oxygen (1O2) in chloroplasts drastic changes in nuclear gene expression occur in the conditional flu mutant of Arabidopsis that reveal a rapid transfer of signals from the plastid to the nucleus. Factors involved in this retrograde signaling were identified by mutagenizing a transgenic flu line expressing a 1O2-responsive reporter gene. The reporter gene consisted of the luciferase open reading frame and the promoter of an AAA-ATPase gene (At3g28580) that was selectively activated by 1O2 but not by superoxide or hydrogen peroxide. A total of eight second-site mutants were identified that either constitutively activate the reporter gene and the endogenous AAA-ATPase irrespectively of whether 1O2 was generated or not (constitutive activators of AAA-ATPase, caa) or abrogated the 1O2-dependent up-regulation of these genes as seen in the transgenic parental flu line (non-activators of AAA-ATPase, naa). The characterization of the mutants strongly suggests that 1O2-signaling does not operate as an isolated linear pathway but rather forms an integral part of a signaling network that is modified by other signaling routes and impacts not only stress responses of plants but also their developmen

Macroscopic Geo-Magnetic Radiation Model; Polarization effects and finite volume calculations

An ultra-high-energy cosmic ray (UHECR) colliding with the Earth's atmosphere gives rise to an Extensive Air Shower (EAS). Due to different charge separation mechanisms within the thin shower front coherent electromagnetic radiation will be emitted within the radio frequency range. A small deviation of the index of refraction from unity will give rise to Cherenkov radiation up to distances of 100 meters from the shower core and therefore has to be included in a complete description of the radio emission from an EAS. Interference between the different radiation mechanisms, in combination with different polarization behavior will reflect in a lateral distribution function (LDF) depending on the orientation of the observer and a non-trivial fall-off of the radio signal as function of distance to the shower core.Comment: Proceedings of the ARENA2010 conference, Nantes, Franc

High-level expression of a viscotoxin in Arabidopsis thaliana gives enhanced resistance against Plasmodiophora brassicae

Viscotoxins are a group of toxic thionins found in several mistletoe species. The constitutive CaMV-Ω promoter was used to drive the expression of the viscotoxin A3 cDNA from Viscum album in transgenic Arabidopsis thaliana C24. Lines with high viscotoxin A3 levels in all parts of the plant were selected and tested for resistance against the clubroot pathogen Plasmodiophora brassicae. The transgenic lines were more resistant to infection by this pathogen than the parental lin

Characterization of soldat8, a Suppressor of Singlet Oxygen-Induced Cell Death in Arabidopsis Seedlings

The flu mutant of Arabidopsis thaliana overaccumulates in the dark the immediate precursor of chlorophyllide, protochlorophyllide (Pchlide), a potent photosensitizer, that upon illumination generates singlet oxygen (1O2). Once 1O2 has been released in plastids of the flu mutant, mature plants stop growing, while seedlings die. Several suppressor mutations, dubbed singlet oxygen-linked death activator (soldat), were identified that specifically abrogate 1O2-mediated stress responses in young flu seedlings without grossly affecting 1O2-mediated stress responses of mature flu plants. One of the soldat mutations, soldat8, was shown to impair a gene encoding the SIGMA6 factor of the plastid RNA polymerase. Reintroduction of a wild-type copy of the SOLDAT8 gene into the soldat8/flu mutant restored the phenotype of the flu parental line. In contrast to flu, seedlings of soldat8/flu did not bleach when grown under non-permissive dark/light conditions, despite their continuous overaccumulation of the photosensitizer Pchlide in the dark. The activity of SIGMA6 is confined primarily to the very early stage of seedling development. Inactivation of SIGMA6 in soldat8 mutants disturbed plastid homeostasis, drastically reduced the non-photochemical quenching capacity and enhanced the light sensitivity of young soldat8 seedlings. Surprisingly, after being grown under very low light, soldat8 seedlings showed an enhanced resistance against a subsequent severe light stress that was significantly higher than in wild-type seedlings. In order to reach a similar enhanced stress resistance, wild-type seedlings had to be exposed to a brief higher light treatment that triggered an acclimatory response. Such a mild pre-stress treatment did not further enhance the stress resistance of soldat8 seedlings. Suppression of 1O2-mediated cell death in young flu/soldat8 seedlings seems to be due to a transiently enhanced acclimation at the beginning of seedling development caused by the initial disturbance of plastid homeostasi