bluuebunny/crossref_metadata_2025 huggingface dataset:
Mad4 is regulated by a transcriptional repressor complex that contains Miz-1 and c-Myc
Authors: KIME Louise , WRIGHT Stephanie C.
Published: February 2003

Myc and Mad family proteins are central regulators of cellular proliferation and differentiation. We show that various Mad family genes have distinct patterns of expression during the chemically induced differentiation of mouse erythroleukaemia (MEL) cells, suggesting that they each serve a different function. Mad4 RNA is highly induced and persists in terminally differentiated cells, in agreement with observations in other systems. Using reporter gene assays in stably transfected MEL cells, we show that induction of Mad4 is mediated by a 49nt core promoter region. We demonstrate that the initiator element is required for Mad4 activation, and show that induction is associated with the loss from the initiator of a complex that contains Miz-1 and c-Myc. Miz-1 activates the Mad4 promoter in transient transfection assays, and this effect is antagonized by c-Myc. We therefore identify Mad4 as a novel target of transcriptional repression by c-Myc. These data suggest that the expression of Mad4 in proliferating undifferentiated cells is suppressed by the binding of a c-Myc—Miz-1 repressor complex at the initiator, and that the activation of Mad4 during differentiation results, at least in part, from a decrease in c-Myc-mediated repression.
Role of superoxide dismutase in survival of Leishmania within the macrophage
Authors: GHOSH Sanjay , GOSWAMI Srikanta , ADHYA Samit
Published: February 2003

Intracellular parasitic protozoans of the genus Leishmania depend for their survival on the elaboration of enzymic and other mechanisms for evading toxic free-radical damage inflicted by their phagocytic macrophage host. One such mechanism may involve superoxide dismutase (SOD), which detoxifies reactive superoxide radicals produced by activated macrophages, but the role of this enzyme in parasite survival has not yet been demonstrated. We have cloned a SOD gene from L. tropica and generated SOD-deficient parasites by expressing the corresponding antisense RNA from an episomal vector. Such parasites have enhanced sensitivity to menadione and hydrogen peroxide in axenic culture, and a markedly reduced survival in mouse macrophages. These results indicate that SOD is a major determinant of intracellular survival of Leishmania.
PDE4 cAMP phosphodiesterases: modular enzymes that orchestrate signalling cross-talk, desensitization and compartmentalization
Authors: HOUSLAY Miles D. , ADAMS David R.
Published: February 2003

cAMP is a second messenger that controls many key cellular functions. The only way to inactivate cAMP is to degrade it through the action of cAMP phosphodiesterases (PDEs). PDEs are thus poised to play a key regulatory role. PDE4 cAMP-specific phosphodiesterases appear to have specific functions with selective inhibitors serving as potent anti-inflammatory agents. The recent elucidation of the structure of the PDE4 catalytic unit allows for molecular insight into the mode of catalysis as well as substrate and inhibitor selectivity. The four PDE4 genes encode over 16 isoforms, each of which is characterized by a unique N-terminal region. PDE4 isoforms play a pivotal role in controlling functionally and spatially distinct pools of cAMP by virtue of their unique intracellular targeting. Targeting occurs by association with proteins, such as arrestins, SRC family tyrosyl kinases, A-kinase anchoring proteins ('AKAPs') and receptor for activated C kinase 1 ('RACK1'), and, in the case of isoform PDE4A1, by a specific interaction (TAPAS-1) with phosphatidic acid. PDE4 isoforms are ‘designed’ to be regulated by extracellular-signal-related protein kinase (ERK), which binds to anchor sites on the PDE4 catalytic domain that it phosphorylates. The upstream conserved region 1 (UCR1) and 2 (UCR2) modules that abut the PDE4 catalytic unit confer regulatory functions by orchestrating the functional outcome of phosphorylation by cAMP-dependent protein kinase ('PKA') and ERK. PDE4 enzymes stand at a crossroads that allows them to integrate various signalling pathways with that of cAMP in spatially distinct compartments.
Activation of S6K1 (p70 ribosomal protein S6 kinase 1) requires an initial calcium-dependent priming event involving formation of a high-molecular-mass signalling complex
Authors: HANNAN Katherine M. , THOMAS George , PEARSON Richard B.
Published: February 2003

The mitogen-stimulated protein kinase p70 ribosomal protein S6 kinase 1 (S6K1) is a key enzyme in the regulation of cell growth and proliferation. Activation of S6K1 requires a complex, ordered series of conformational changes and phosphorylation reactions. While the role of sequential, multi-site phosphorylation has been extensively detailed, characterization of the priming step required to initiate this cascade has remained elusive. In the present study we show for the first time that this priming process is dependent on calcium. Calcium-dependent regulation of S6K1 did not specifically target Thr-229 and Thr-389, the key regulatory phosphorylation sites; rather, calcium chelation resulted in a global inhibition of S6K1 phosphorylation. Mutation of individual phosphorylation sites in the auto-inhibitory and hydrophobic domains to acidic residues (to mimic phosphorylation) yields a kinase that remains sensitive to calcium chelation, while the combined mutations alleviate the requirement for calcium. Furthermore, deletion of the C-terminal residues (398—502) also renders the kinase insensitive to calcium. We hypothesize that the initial calcium-dependent process is required to release an inhibitory interaction between the C- and N-termini of S6K1, thus allowing phosphorylation of these key domains. The requirement for this priming step can only be overcome by mutations mimicking the phosphorylation of both the auto-inhibitory and hydrophobic domains. We further propose that the priming event involves formation of a calcium-dependent protein complex that releases the interaction between the N- and C-termini. S6K1 is then accessible for activation by the kinases that target the known regulatory phosphorylation sites. Consistent with this hypothesis, serum stimulation of S6K1 activity is associated with its incorporation into a calcium-dependent high-molecular-mass complex.
Detection of HOCl-mediated protein oxidation products in the extracellular matrix of human atherosclerotic plaques
Authors: WOODS Alan A. , LINTON Stuart M. , DAVIES Michael J.
Published: February 2003

Oxidation is believed to play a role in atherosclerosis. Oxidized lipids, sterols and proteins have been detected in early, intermediate and advanced human lesions at elevated levels. The spectrum of oxidized side-chain products detected on proteins from homogenates of advanced human lesions has been interpreted in terms of the occurrence of two oxidative mechanisms, one involving oxygen-derived radicals catalysed by trace transition metal ions, and a second involving chlorinating species (HOCl or Cl2), generated by the haem enzyme myeloperoxidase (MPO). As MPO is released extracellularly by activated monocytes (and possibly macrophages) and is a highly basic protein, it would be expected to associate with polyanions such as the glycosaminoglycans of the extracellular matrix, and might result in damage being localized at such sites. In this study proteins extracted from extracellular matrix material obtained from advanced human atherosclerotic lesions are shown to contain elevated levels of oxidized amino acids [3,4-dihydroxyphenylalanine (DOPA), di-tyrosine, 2-hydroxyphenylalanine (o-Tyr)] when compared with healthy (human and pig) arterial tissue. These matrix-derived materials account for 83—96% of the total oxidized protein side-chain products detected in these plaques. Oxidation of matrix components extracted from healthy artery tissue, and model proteins, with reagent HOCl is shown to give rise to a similar pattern of products to those detected in advanced human lesions. The detection of elevated levels of DOPA and o-Tyr, which have been previously attributed to the occurrence of oxygen-radical-mediated reactions, by HOCl treatment, suggests an alternative route to the formation of these materials in plaques. This is believed to involve the formation and subsequent decomposition of protein chloramines.
In vitro fusion between Saccharomyces cerevisiae secretory vesicles and cytoplasmic-side-out plasma membrane vesicles
Authors: ARRASTUA Lorena , SEBASTIAN Eider SAN , QUINCOCES Ana F. , ANTONY Claude , UGALDE Unai
Published: February 2003

The final step in the secretory pathway, which is the fusion event between secretory vesicles and the plasma membrane, was reconstructed using highly purified secretory vesicles and cytoplasmic-side-out plasma membrane vesicles from the yeast Saccharomyces cerevisiae. Both organelle preparations were obtained from a sec 6-4 temperature-sensitive mutant. Fusion was monitored by means of a fluorescence assay based on the dequenching of the lipophilic fluorescent probe octadecylrhodamine B-chloride (R18). The probe was incorporated into the membrane of secretory vesicles, and it diluted in unlabelled cytoplasmic-side-out plasma membrane vesicles as the fusion process took place. The obtained experimental dequenching curves were found by mathematical analysis to consist of two independent but simultaneous processes. Whereas one of them reflected the fusion process between both vesicle populations as confirmed by its dependence on the assay conditions, the other represented a non-specific transfer of the probe. The fusion process may now be examined in detail using the preparation, validation and analytical methods developed in this study.
A sulphoquinovosyl diacylglycerol is a DNA polymerase epsilon inhibitor
Authors: MIZUSHINA Yoshiyuki , XU Xianai , ASAHARA Hitomi , TAKEUCHI Ryo , OSHIGE Masahiko , SHIMAZAKI Noriko , TAKEMURA Masaharu , YAMAGUCHI Toyofumi , KURODA Kazufumi , LINN Stuart , YOSHIDA Hiromi , KOIWAI Osamu , SANEYOSHI Mineo , SUGAWARA Fumio , SAKAGUCHI Kengo
Published: February 2003

Sulphoquinovosyl diacylglycerol (SQDG) was reported as a selective inhibitor of eukaryotic DNA polymerases α and β [Hanashima, Mizushina, Ohta, Yamazaki, Sugawara and Sakaguchi (2000) Jpn. J. Cancer Res. 91, 1073—1083] and an immunosuppressive agent [Matsumoto, Sahara, Fujita, Shimozawa, Takenouchi, Torigoe, Hanashima, Yamazaki, Takahashi, Sugawara et al. (2002) Transplantation 74, 261—267]. The purpose of this paper is to elucidate the biochemical properties of the inhibition more precisely. As expected, SQDG could inhibit the activities of mammalian DNA polymerases such as α, Δ, η and κ in vitro in the range of 2—5μM, and β and λ in vitro in the range of 20—45μM. However, SQDG could inhibit only mammalian DNA polymerases ∊ (pol ∊) activity at less than 0.04μM. SQDG bound more tightly to mammalian pol ∊ than the other mammalian polymerases tested. Moreover, SQDG could inhibit the activities of all the polymerases from animals such as fish and insect, but not of the polymerases from plant and prokaryotes. SQDG should, therefore, be called a mammalian pol ∊-specific inhibitor or animal polymerase-specific inhibitor. To our knowledge, this represents the first report about an inhibitor specific to mammalian pol ∊.
Genomic identification and biochemical characterization of the mammalian polyamine oxidase involved in polyamine back-conversion
Authors: VUJCIC Slavoljub , LIANG Ping , DIEGELMAN Paula , KRAMER Debora L. , PORTER Carl W.
Published: February 2003

In the polyamine back-conversion pathway, spermine and spermidine are first acetylated by spermidine/spermine N1-acetyltransferase (SSAT) and then oxidized by polyamine oxidase (PAO) to produce spermidine and putrescine respectively. Although PAO was first purified more than two decades ago, the protein has not yet been linked to genomic sequences. In the present study, we apply a BLAST search strategy to identify novel oxidase sequences located on human chromosome 10 and mouse chromosome 7. Homologous mammalian cDNAs derived from human brain and mouse mammary tumour were deduced to encode proteins of approx. 55kDa having 82% sequence identity. When either cDNA was transiently transfected into HEK-293 cells, intracellular spermine pools decreased by approx. 30%, whereas spermidine increased 2—4-fold. Lysates of human PAO cDNA-transfected HEK-293 cells, but not vector-transfected cells, rapidly oxidized N1-acetylspermine to spermidine. Substrate specificity determinations with the lysate assay revealed a preference ranking of N1-acetylspermine = N1-acetylspermidine>N1,N12-diacetylspermine>spermine; spermidine was not acted upon. This ranking is identical to that reported for purified PAO and distinctly different from the recently identified spermine oxidase (SMO), which prefers spermine over N1-acetylspermine. Monoethyl- and diethylspermine analogues also served as substrates for PAO, and were internally cleaved adjacent to a secondary amine. We deduce that the present oxidase sequences are those of the FAD-dependent PAO involved in the polyamine back-conversion pathway. In Northern blot analysis, PAO mRNA was much less abundant in HEK-293 cells than SMO or SSAT mRNA, and all three were differentially induced in a similar manner by selected polyamine analogues. The identification of PAO sequences, together with the recently identified SMO sequences, provides new opportunities for understanding the dynamics of polyamine homoeostasis and for interpreting metabolic and cellular responses to clinically-relevant polyamine analogues and inhibitors.
Gene disruption discloses role of selenoprotein P in selenium delivery to target tissues
Authors: SCHOMBURG Lutz , SCHWEIZER Ulrich , HOLTMANN Bettina , FLOHÉ Leopold , SENDTNER Michael , KÖHRLE Josef
Published: February 2003

Selenoprotein P (SePP), the major selenoprotein in plasma, has been implicated in selenium transport, selenium detoxification or antioxidant defence. We generated SePP-knockout mice that were viable, but exhibited reduced growth and developed ataxia. Selenium content was elevated in liver, but low in plasma and other tissues, and selenoenzyme activities changed accordingly. Our data reveal that SePP plays a pivotal role in delivering hepatic selenium to target tissues.
Cloning of a new type II cytokine receptor activating signal transducer and activator of transcription (STAT)1, STAT2 and STAT3
Authors: DUMOUTIER Laure , LEJEUNE Diane , HOR Simon , FICKENSCHER Helmut , RENAULD Jean-Christophe
Published: February 2003

In the present paper, we report the identification of a new gene encoding a transmembrane protein of 520 amino acids, showing 22% amino acid identity with the extracellular domain of the interleukin (IL)-20 receptor. This gene, termed likely interleukin or cytokine receptor-2 (LICR2), is located on chromosome 1, at 25kb from the IL22R (IL-22 receptor) gene, and is constitutively expressed in most tissues. A chimaeric receptor, consisting of the extracellular domain of the IL-10 receptorα chain and the intracellular domain of LICR2, activated signal transducer and activator of transcription (STAT)1, STAT2, STAT3 and STAT5 upon IL-10 stimulation, in a Janus kinase 1-dependent manner. In contrast, none of the IL-10-related cytokines described so far could activate LICR2-transfected cells, suggesting that LICR2 is a signalling receptor for a new cytokine of the IL-10 family.
Photosynthetic Characteristics of Eastern Dwarf Mistletoe (Arceuthobium pusillum Peck) and its Effects on the Needles of Host White Spruce (Picea glauca [Moench] Voss)
Authors: Logan B. A. , Huhn E. R. , Tissue D. T.
Published: February 2003

Abstract: We studied the biochemical composition and photosynthetic characteristics of the aerial parasite eastern dwarf mistletoe (Arceuthobium pusillum) and the effect of infection on the needles of host white spruce (Picea glauca) in a coastal forest stand in Maine, USA. Eastern dwarf mistletoe was capable of photosynthetic oxygen evolution; however, rates were low and were exceeded by respiratory oxygen consumption at all light intensities through full sunlight. Therefore, eastern dwarf mistletoe acts as a net sink for host photosynthate. Relative to those of uninfected trees, needles from infected branches of white spruce were significantly smaller in terms of length, fresh weight, maximum cross section and the diameter of the vascular cylinder. Needles of uninfected and infected trees did not differ in terms of fresh weight to dry weight ratio, nor in nitrogen, soluble sugar or starch content. Needles of infected trees possessed significantly less α‐carotene and neoxanthin, but did not otherwise differ from uninfected needles in terms of chlorophyll and carotenoid composition. Since specific physiological roles for α‐carotene and neoxanthin have not been described, the functional significance of the decreases in their content is not known. Photosynthetic capacities of needles from infected and uninfected white spruce did not differ significantly, as measured by oxygen evolution. These findings suggest that dwarf mistletoe infection does not substantially perturb host white spruce source‐sink balance at the end of the growing season and that carbon exchange dynamics between the host and parasite are unlikely to fully explain the detrimental effects of infection on white spruce.
Brassinosteroids as Metahormones: Evidence for their Specific Influence during the Critical Period in Sorghum Development
Authors: Amzallag G. N.
Published: February 2003

Abstract: In Sorghum bicolor, the effect of brassinosteroid (BR) treatments on blade elongation depends both on concentration and on the stage of development. A specific period of increase in sensitivity to BR is reported during early vegetative development. It coincides with emergence of a critical period during which the between‐organs relationship is readjusted as a function of new developmental events or new environmental conditions. Accordingly, the influence of BR cannot be completely understood without separating its effects during stable phases (phenophases) and during critical periods. A high level of redundancy exists in networks of regulation, so that modifications due to BR treatments generally remain cryptic. Nevertheless, it is shown that BR affects the pattern of relationships between organs, confirming its involvement in emergence of a new network of regulation. It is suggested that, during critical periods, brassinosteroids act as “metahormones” integrating the new emerging regulation network by triggering changes in cellular sensitivity to PGRs.
Analysis of Cytosine Methylation Pattern in Response to Water Deficit in Pea Root Tips
Authors: Labra M. , Ghiani A. , Citterio S. , Sgorbati S. , Sala F. , Vannini C. , Ruffini‐Castiglione M. , Bracale M.
Published: February 2003

Abstract: The correlation between environmental stress and DNA methylation has been studied by following the methylation status of cytosine residues in the DNA of pea root tips exposed to water deficit. DNA methylation was evaluated by two complementary approaches: (i) immunolabelling by means of a monoclonal antibody against 5‐methylcytosine; (ii) MSAP (Methylation‐Sensitive Amplified Polymorphism) to verify if methylation and de‐methylation in response to water deficit may be related to specific DNA sequences. Immunolabelling showed that water stress induces cytosine hypermethylation in the pea genome. Regarding the CCGG target sequence, an increase in methylation specifically in the second cytosine (about 40 % of total site investigated) was revealed by MSAP analyses. In addition, MSAP band profile detected in three independent repetitions was highly reproducible suggesting that, at least for the CCGG target sequence, methylation was addressed to specific DNA sequences.
Evaluation of Transgenic Poplars Over‐Expressing Enzymes of Glutathione Synthesis for Phytoremediation of Cadmium
Authors: Koprivova A. , Kopriva S. , Jäger D. , Will B. , Jouanin L. , Rennenberg H.
Published: February 2003

Abstract: Recently, phytoremediation of soils polluted with heavy metals has received a lot of attention. Since glutathione (GSH) and its derivatives (e.g., phytochelatins) play a major role in plant defence against environmental pollutants, we tested the effects of over‐expression of bacterial genes for GSH synthesis in poplar on cadmium accumulation. A pilot experiment with CdCl2 in hydroponics revealed that poplars over‐expressing γ‐glutamylcysteine synthetase (γ‐ECS) accumulated significantly more Cd in root tissue than wild type or glutathione synthetase over‐expressing poplars. To test the partitioning of Cd in different organs, poplar lines over‐expressing γ‐ECS in the cytosol and in chloroplasts were treated with 0.2 mM CdCl2 in hydroponics. Significant amounts of Cd were translocated to leaves, but significant differences in Cd accumulation were not observed between transgenic and wild type plants. To evaluate these lines for large‐scale phytoremediation of cadmium, plants were treated with 2 mM Cd in soil. Over a four‐week period, the poplar plants were able to accumulate up to 5.3 mg Cd. Most remarkably, in young leaves of both transgenic lines, Cd was accumulated to concentrations 2.5 ‐ 3 times higher than in the wild type. The increased allocation of cadmium to the young leaves represents a potentional advantage for the phytoremediation process using the same plants over several vegetation periods. The use of transgenic poplar lines with enhanced glutathione production capacity seems to be of particular advantage in highly polluted soils.
Effects of Small Habitat Size and Isolation on the Population Structure of Common Wetland Species
Authors: Hooftman D. A. P. , Diemer M.
Published: February 2003

Abstract: Habitat fragmentation may cause plant species to suffer from inbreeding and genetic drift, which affects population viability negatively. Less viable populations may contain an altered population structure, i.e., they have a smaller proportion of seedlings and a larger proportion of vegetative adults, when compared to large extensive populations. We applied a hierarchical‐spatial field design, consisting of large habitat islands with surrounding near and distant small habitat islands to distinguish between the two components of habitat fragmentation, i.e., the effect of small habitat size and the effect of isolation. We studied two common habitat‐specific species: Carex davalliana (Cyperaceae) and Succisa pratensis (Dipsacaceae). We identified a decrease in the proportion of C. davalliana seedlings and an increase in the proportion of vegetative tillers in response to isolation. In S. pratensis, we identified a decrease in the proportion of seedlings and an increase in the proportion of vegetative rosettes that were attributable to small habitat size. Hence, we confirmed alterations in the population structure of those common species, although both species were affected by a different component of habitat fragmentation. The observed discrepancy between species could be related their life history. We conclude that habitat fragmentation adversely affects not only rare but also common species. Their loss of viability can inevitably lead to alterations in vegetation structure and consequently lead to the further loss of this species‐rich and threatened ecosystem type.
Physiological Comparisons among Four Related Bromus Species with Varying Ecological Amplitude: Polyamine and Aromatic Amine Composition in Response to Salt Spray and Drought
Authors: Gicquiaud L. , Hennion F. , Esnault M.‐A.
Published: February 2003

Abstract: We examined the amine composition in response to experimental osmotic or salt treatments of populations from four related Bromus species in relation to the environment of their origin. We studied populations from (1) a sand dune protected from salt spray, and (2) a sand dune subject to salt spray. The study of amine composition and contents, the first in Bromus, revealed a significant effect of origin for Spd and slightly for Spm, and higher levels were found in offspring of plants originating from an environment subject to sea spray. In all populations and species, plants subjected to osmotic and salt treatments showed significant decreases in Put, Spd, Spm and Dop levels. This was accompanied by significant increases in the oxidation product Dap and the amplitude of this response coincided with the presence of salt spray observed in the environment of origin of seeds, except for populations of B. rigidus. Interspecific differences in amine composition and contents were also detected. Higher levels of Tyr and Dop were found in B. sterilis and B. diandrus, respectively. For Dap and Tyr, B. rigidus, the species with the narrowest ecological amplitude in Brittany, showed the lowest response to either treatment. Our study of amine variations in Bromus populations and species illustrate the links between the amplitude of amine response to experimental salt or osmotic treatments and (1) the exposure of populations to sea spray; and (2) the ecological amplitude of Bromus species. Finally, experimental stress resulted in a strong decrease of interspecific variability in relation to amine metabolism in these four species.
Genetic Variation of Sesleria albicans Kit. ex Schultes (Poaceae): Lack of Evidence for Glacial Relict Endemism in Central Europe
Authors: Reisch C. , Poschlod P. , Wingender R.
Published: February 2003

Abstract: The populations of Sesleria albicans Kit. ex Schultes in central Europe are supposed to be glacial relicts. The genetic structure of these populations can provide evidence for the reliability of this hypothesis, since a distinct geographical clustering of populations and high levels of interpopulational genetic variation can be expected in the case of relict endemism. In the study presented here, we used Random Amplified Polymorphic DNA (RAPD) analysis to describe the genetic structure of 25 Sesleria albicans populations from west and central Germany, southwest Germany and the Alps. In the RAPD analysis 344 fragments could be amplified, of which 95.9 % were polymorphic. The percentage of polymorphic bands per population ranged from 29.7 % to 56.7 % and correlated significantly with population size, indicating a higher level of inbreeding in small and isolated populations. An analysis of molecular variance (AMOVA) revealed that 61.22 % of the variation resided within populations, whereas 34.25 % was found among populations within regions and only 4.53 % among regions. Genetic distance among populations (φST) varied between 0.63 and 0.13, and in a Neighbour‐Joining dendrogram based on the genetic distances between the investigated individuals, all populations could be discriminated from each other. The populations from the northern and southern Alps were clearly separated from the central European populations. These, however, did not form geographic clusters. Considering these results, Sesleria albicans showed a high level of intra‐ but only a low level of interpopulational genetic variation and very weak regional differentiation. The genetic pattern detected in this study, therefore, gives no evidence for glacial relict endemism of Sesleria albicans in central Europe.
Epiphytic Bacteria Associated with the Bryophyte Funaria hygrometrica: Effects of Methylobacterium Strains on Protonema Development
Authors: Hornschuh M. , Grotha R. , Kutschera U.
Published: February 2003

Abstract: Bacteria represent a substantial fraction of the microorganisms that inhabit leaf surfaces. We collected samples of the moss Funaria hygrometrica (L.) in the field and analysed the epiphytes on the gametophyte by the agar impression method and scanning electron/fluorescence microscopy. On the phylloid surface numerous bacteria were detected, notably in the grooves between adjacent lamina cells. Methanol‐ammonium salts agar surfaces impressed with isolated phylloids of green gametophytes resulted in the growth of methylotrophic colonies. Two Methylobacterium strains (M. mesophilicum and M. sp., isolated from the Funaria phylloids) were found to simulate the well‐known effect of cytokinin application on bud formation in Funaria protonemata. In addition, Methylobacterium inoculation promoted the growth of protonemal filaments. The significance of this novel Methylobacterium‐land plant interaction is discussed.
The Pneumathodes ofLaguncularia racemosa:Little Known Rootlets of Surprising Structure, and Notes on a New Fluorescent Dye for Lipophilic Substances
Authors: Geiβler N. , Schnetter R. , Schnetter M.‐L.
Published: February 2003

Abstract:Two types of negatively geotropic aerial roots may be observed on the root system ofLaguncularia racemosa:pneumatophores with secondary growth, and short‐lived pneumathodes which remain in the primary anatomical state. The pneumathodes distinguish themselves by the absence of an epidermis; instead, the outer cortex takes the place of the outermost tissue. This tissue forms a three‐dimensional network of rod‐like cells and gas spaces. The cell walls contain a lipophilic substance which ensures that the intercellular spaces remain gas‐filled during submergence. An uniseriate cellular layer separates the outer and inner cortex. This uniseriate cellular layer, which we term a “pore layer”, is characterized by cells with suberized and lignified cell walls and occasional pores among the cells. The pores permit the diffusion of oxygen‐rich air from the surface of the pneumathode to the aerenchyma of the inner cortex and the escape of carbon dioxide from the interior of the root. The structure of the differentiated pneumathode originates from frequent cell divisions in the part of the apical meristem where the outer cortex emerges. Because of the pressure thereby exerted on the epidermis and hypodermis, these two cell layers tear and become separated from the outer cortex. Their remnants remain visible at the base of the pneumathode and as an appendage of the calyptra. The function and significance of the pneumathodes forL. racemosaare discussed. An extract ofXanthoria parietinawas employed as a new fluorescent dye to stain suberine in cell walls. The staining technique is presented in this paper.
EST Sequencing, Annotation and Macroarray Transcriptome Analysis Identify Preferentially Root‐Expressed Genes in Sugar Beet
Authors: Bellin D. , Werber M. , Theis T. , Schulz B. , Weisshaar B. , Schneider K.
Published: February 2003

Abstract: An integrated approach involving EST sequencing, data mining and multiparallel expression profiling by macroarray analysis was established to classify sugar beet gene products with respect to their expression in three different organs. The DNA sequences of 2996 ESTs derived from young sugar beet plants specified 2048 unique gene products with putative functions in primary and secondary metabolism (651), transport processes (136), signal transduction (78) and cellular organization (39). The cDNA clone collection was the basis for the generation of a macroarray. Sensitivity and reproducibility of our macroarray hybridization procedure were estimated first. The detection limit was found to correspond to 10 ‐ 50 copies of single transcripts per cell. Within an interval of two‐fold variation in signal intensities, reproducibility between spots on the same filter was determined to be 98.9 %, between spots on different filters 89.8 %, and reproducibility after hybridization with two probes synthesized from the same poly(A)+RNA sample was 97.6 %. Expression profiles from roots, leaves and inflorescences of field‐grown plant material were generated. Two different samples of each organ were analysed to reduce sampling effects, which accounted on average for 30.3 % of spots with at least two‐fold deviation. Expression values for each organ were determined by a stringent statistical evaluation of eight hybridizations for each clone. Macroarray expression data were confirmed by Northern blot analysis and quantitative RT‐PCR experiments concerning eleven cDNAs. The analysis was then focused on 76 unique cDNAs, for which the amount of detected transcript in roots was at least twice as high as in the other organs tested. Functions of preferentially root‐expressed candidate genes in taproot morphology and physiology are discussed.
Clonal Differences in the Formation of Turions are Independent of the Specific Turion‐inducing Signal in Spirodela polyrhiza (Great Duckweed)
Authors: Appenroth K.‐J.
Published: February 2003

Abstract: Turion (survival organ) formation in Spirodela polyrhiza includes a switch in the programming of the primordia from the formation of vegetative fronds toward resting turions. The specific turion yield (SY; number of turions formed by one frond) is used to evaluate the effect of three turion‐inducing signals: low phosphate concentration (depleted due to frond growth), low temperature (15 °C) and exogenously applied abscisic acid (1 μM). The formation of turions was observed in the presence of any of the turion‐inducing factors in all three clones of S. polyrhiza investigated (clones 9256 from Finland, SJ from Germany and SC from Cuba). The clone SC showed no specific induction by low temperature or phosphate limitation in one nutrient medium. Regardless of the specific signal applied, the SYs were highest in clone 9256 and lowest in clone SC, demonstrating signal‐independent clonal differences. Clonal differences are therefore located in the developmental‐specific common phase of the transduction chains leading to turion formation. We intend to use clonal differences in the molecular analysis of turion formation, e.g., by cDNA‐based amplified fragment length polymorphism, to distinguish signal‐specific and developmental‐specific gene expression. In contrast, the total turion yield is useful in an ecological context to evaluate the number of turions available to support the survival of a population of plants but gives little information about the physiological process.
Mtha1, a Plasma Membrane H+‐ATPase Gene from Medicago truncatula, Shows Arbuscule‐Specific Induced Expression in Mycorrhizal Tissue
Authors: Krajinski F. , Hause B. , Gianinazzi‐Pearson V. , Franken P.
Published: February 2003

Abstract: Transport processes between plant and fungal cells are key elements in arbuscular mycorrhiza (AM), where H+‐ATPases are considered to be involved in active uptake of nutrients from the symbiotic interface. Genes encoding H+‐ATPases were identified in the genome of Medicago truncatula and three cDNA fragments of the H+‐ATPase gene family (Mtha1 ‐ 3) were obtained by RT‐PCR using RNA from M. truncatula mycorrhizal roots as template. While Mtha2 and Mtha3 appeared to be constitutively expressed in roots and unaffected by AM development, transcripts of Mtha1 could only be detected in AM tissues and not in controls. Further analyses by RT‐PCR revealed that Mtha1 transcripts are not detectable in shoots and phosphate availability did not affect RNA accumulation of the gene. Localization of transcripts by in situ hybridization on AM tissues showed that Mtha1 RNA accumulates only in cells containing fungal arbuscules. This is the first report of arbuscule‐specific induced expression of a plant H+‐ATPase gene in mycorrhizal tissues.
High‐Resolution Chlorophyll Fluorescence Imaging Serves as a Non‐Invasive Indicator to Monitor the Spatio‐Temporal Variations of Metabolism during the Day‐Night Cycle and during the Endogenous Rhythm in Continuous Light in the CAM Plant Kalanchoë daigremontiana
Authors: Rascher U. , Lüttge U.
Published: February 2003

Abstract: Chlorophyll fluorescence imaging is a powerful tool to monitor temporal and spatial dynamics of photosynthesis and photosynthesis‐related metabolism. In this communication, we use high resolution chlorophyll fluorescence imaging techniques under strictly controlled conditions to quantify day courses of relative effective quantum yield (ϕPSII) of an entire leaf of the crassulacean acid metabolism (CAM) plant Kalanchoë daigremontiana at different light intensities. Careful interpretation of the combined gas exchange and fluorescence data, in combination with micro malate samples, allow the interpretation of underlying metabolic properties, such as leaf internal CO2 concentration (ciCO2) and energy demand of the cells. Spatial variations of ϕPSII, which occur as running wave fronts at the transition from phase III to phase IV of CAM, may reflect spatial differences of ciCO2, which are preserved in the tightly packed mesophyll cells of K. daigremontiana. An endogenous rhythm is driven by a master switch which mediates between malate storage and malate release to and from the vacuole, however, using fluorescence techniques, four different metabolic states can be distinguished which also account for the activity of phosphoenolpyruvate carboxylase.
Breakdown behavior in radio-frequency argon discharges
Authors: Smith H. B. , Charles C. , Boswell R. W.
Published: February 2003

The minimum voltage required to break down a discharge Vbrk has long been known to be a strong function of the product of the neutral gas pressure and the electrode separation (pd). This paper investigates the dependence of Vbrk on pd in radio-frequency (rf) systems using experimental, computational and analytic techniques. Experimental measurements of Vbrk in an argon discharge are made for pressures in the range 1–500 mTorr and electrode separations of 2–20 cm. A particle-in-cell simulation is used to investigate a similar pd range and examine the effect of the secondary emission coefficient on the rf breakdown curve, particularly at low pd values. A zero- dimensional global (volume averaged) model is also developed to compare with experimental and simulated measurements of breakdown.
The time scale for the transition to turbulence in a high Reynolds number, accelerated flow
Authors: Robey H. F. , Zhou Ye , Buckingham A. C. , Keiter P. , Remington B. A. , Drake R. P.
Published: February 2003

An experiment is described in which an interface between materials of different density is subjected to an acceleration history consisting of a strong shock followed by a period of deceleration. The resulting flow at this interface, initiated by the deposition of strong laser radiation into the initially well characterized solid materials, is unstable to both the Richtmyer–Meshkov (RM) and Rayleigh–Taylor (RT) instabilities. These experiments are of importance in their ability to access a difficult experimental regime characterized by very high energy density (high temperature and pressure) as well as large Reynolds number and Mach number. Such conditions are of interest, for example, in the study of the RM/RT induced mixing that occurs during the explosion of a core-collapse supernova. Under these experimental conditions, the flow is in the plasma state and given enough time will transition to turbulence. By analysis of the experimental data and a corresponding one-dimensional numerical simulation of the experiment, it is shown that the Reynolds number is sufficiently large (Re>105) to support a turbulent flow. An estimate of three key turbulence length scales (the Taylor and Kolmogorov microscales and a viscous diffusion scale), however, shows that the temporal duration of the present flow is insufficient to allow for the development of a turbulent inertial subrange. A methodology is described for estimating the time required under these conditions for the development of a fully turbulent flow.
Multidimensional calculation of time-resolved photoelectron angular distributions: The internal conversion dynamics of pyrazine
Authors: Suzuki Yoshi-ichi , Stener Mauro , Seideman Tamar
Published: February 2003

We present the first calculation of time-resolved photoelectron differential cross sections for a polyatomic molecule. The calculation is based on a nonperturbative quantum mechanical theory that accounts exactly for rotations and vibrations and describes the electronic dynamics within a density functional approach. Application is made to study the dynamics of a radiationless transition, as probed by time-resolved photoelectron imaging. Specifically, we consider the ultrafast S2→S1 internal conversion of pyrazine, induced by a short excitation pulse and probed by a time-delayed ionization pulse. Through calculation of total ionization signals, photoelectron energy distributions and energy-integrated and -resolved photoelectron angular distributions, we explore the potential of time-resolved photoelectron imaging. By comparing several models of the ionization dynamics, we examine the extent to which time-resolved photoelectron imaging can provide a general probe of ultrafast nonradiative transitions.
Dispersive shallow water magnetohydrodynamics
Authors: Dellar Paul J.
Published: February 2003

Shallow water magnetohydrodynamics (SWMHD) is a recently proposed model for a thin layer of incompressible, electrically conducting fluid. The velocity and magnetic field are taken to be nearly two dimensional, with approximate magnetohydrostatic balance in the perpendicular direction, leading to a reduced two-dimensional model. The SWMHD equations have been found previously to admit unphysical cusp-like singularities in finite amplitude magnetogravity waves. This paper extends the Hamiltonian formulation of SWMHD to construct a dispersively regularized system, analogous to the Green–Naghdi equations of hydrodynamics, that supports smooth solitary waves and cnoidal wave trains, and shares the potential vorticity conservation properties of SWMHD.
Edge dimensionless identity experiment on DIII-D and Alcator C-Mod
Authors: Mossessian D. A. , Groebner R. J. , Moyer R. A. , Osborne T. H. , Hughes J. W. , Greenwald M. , Hubbard A. , Rhodes T. L.
Published: February 2003

Experiments were carried out to study the similarity of H-mode (high confinement mode) physics on the Alcator C-Mod [I. H. Hutchinson et al., Phys. Plasmas 1, 1511 (1994)] and DIII-D [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] tokamaks comparing plasmas with matched local edge dimensionless parameters (β, ρ*, ν*, q95) and shape (ε, κ, δ). It was observed that matching local values of the dimensionless parameters on top of the H-mode pedestals produces similar Te and ne profiles across the entire pedestal region, with pedestal width scaling linearly with the machine size. Furthermore, in H-modes with matched pedestals, similar edge fluctuations were observed. Discharges in DIII-D with scaled pedestal parameters similar to those of C-Mod EDA (enhanced D-alpha) H-mode showed a quasicoherent mode localized to the outer half of the pedestal, similar to the C-Mod quasicoherent mode (QC mode). The wavenumber of the mode observed on DIII-D matches the wavenumber of the C-Mod QC mode if scaled with the machine size. For higher pedestal temperatures and pressures, small high frequency edge localized modes appear in both machines.
A statistical analysis of pulsed poloidal current drive in the Reversed Field eXperiment
Authors: Cravotta A. , Spizzo G. , Terranova D. , Bolzonella T. , Franz P. , Marrelli L. , Martin P. , Martini S. , Ortolani S.
Published: February 2003

Pulsed poloidal current drive (PPCD) experiments have been performed in the reversed-field pinch device RFX [G. Rostagni, Fus. Eng. Design 25, 301 (1995)], with various control techniques of the edge toroidal field. A detailed statistical analysis has been performed over ∼430 RFX pulses and is presented in this paper. We have found that the temperature increase and m=1 fluctuations reduction scale with the applied electric field Eθ, which is a control parameter for plasma performances. Soft x-ray imaging shows an increase in the core, where often an m=1 helical coherent structure appears, similar to those observed during quasi-single helicity states in RFX. These phenomena are ultimately linked to the magnetic turbulence reduction and q profile modifications that take place during PPCD in the reversed-field pinch.
Phenomenology of internal reconnections in the National Spherical Torus Experiment
Authors: Semenov I. , Mirnov S. , Darrow D. , Roquemore L. , Fredrickson E. D. , Menard J. , Stutman D. , Belov A.
Published: February 2003

The behavior of large scale magnetohydrodynamic modes was investigated in the National Spherical Torus Experiment (NSTX) [M. Ono et al., Nucl. Fusion 40, 557 (2000)] during reconnection events using combined analysis of magnetic probe signals, and soft x-ray data. The comparison of mode dynamics during precursor and disruption stages in T-11M (V. S. Vlasenkov et al., in Proceedings of the 6th International Conference on Plasma Physics and Controlled Nuclear Fusion Research, Berchtesgaden, 6–13 October 1976, p. 95) (small circular plasma), Tokamak Fusion Test Reactor [R. J. Hawryluk et al., Plasma Phys. Controlled Fusion 33, 1509 (1991)] (large circular plasma), and NSTX (large spherical plasma) was done. The analysis shows that the sequence of events of minor and major internal reconnection events (IRE) in NSTX is essentially similar to that for disruptions in moderate aspect ratio tokamaks. The main feature of disruption dynamics apparently affected by the small aspect ratio in NSTX appears in the relatively slow thermal quench event (5–10 times longer compared to ordinary tokamaks), which precedes the major IRE. The coincidence of the electron and neutron quench times during the major IRE leads us to the conclusion that the fast ions and hot electrons leave the center of a plasma column simultaneously, i.e., convectively.
Hysteresis and relaxation in bistable diffusive sandpile
Authors: Gruzinov I. , Diamond P. H. , Rosenbluth M. N.
Published: February 2003

Several problems in the physics of L→H transition and pedestal formation are examined using a simple and universal sandpile model, which incorporates key features of a confined plasma, namely, diffusion, shear induced bistability of turbulent transport, and a local magnetohydrodynamic (MHD) limit on the gradient. The main focus of this study is the effect of ambient diffusion, representative of neoclassical transport, on hysteresis and edge relaxation phenomena. The transport function of the sandpile bifurcates to a multivalued function with increasing deposition, and, as a consequence, a hysteresis in the L→H→L transition is observed. With pedestal formation, diffusive losses increase at the expense of the turbulent flux. This effect prolongs the time needed to reach the MHD stability boundary, and thus provides a positive feedback on the pedestal. The gradient in the pedestal is more rigid and, due to diffusive smoothing, can reach the critical value at all radii simultaneously. Hence an avalanche, starting at the edge, can span the entire pedestal, thus destroying it. The transport in the core is essentially unaffected by the diffusion.
Mechanism of radial redistribution of energetic trapped ions due to m=2/n=1 kink instability in plasmas with an internal transport barrier in the Joint European Torus
Authors: Gorelenkov N. N. , Gondhalekar A. , Korotkov A. A. , Sharapov S. E. , Testa D. ,   Contributors to the EFDA-JET Workprogramme
Published: February 2003

Internal radial redistribution of MeV energy ion cyclotron resonance frequency driven hydrogen minority ions was inferred from neutral particle analyzer measurements during large amplitude magnetohydrodynamic activity in plasmas with an internal transport barrier in the Joint European Torus. A theory is developed for energetic ion redistribution during a m=2/n=1 kink mode instability. Plasma motion during the instability or during subsequent magnetic reconnection generates an electric field which can change the energy and radial position of the energetic ions. The magnitude of ion energy change depends on the value of the safety factor at the plasma core, q(0) from which the energetic ions are redistributed. A relation is found for the corresponding change in canonical momentum Pφ, which leads to radial displacement of the ions. The model yields distinctive new features of energetic ion redistribution such as more vertical particle displacement as q(0) increases from 1 to 2. Predicted characteristics of ion redistribution are compared with the measurements, and good correlation is found. Sometimes the energetic ions were further transported to the plasma edge due to interaction with a long-lived magnetic fluctuation (often in the form of a magnetic island) with chirping frequency in the laboratory frame which developed after the m=2/n=1 kink instability. Convection of resonant ions trapped in a radially moving phase-space island is modeled to understand the physics of such events.