bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of an X family DNA polymerase in double‐stranded break repair in the radioresistant organism Deinococcus radiodurans
Authors: Lecointe François , Shevelev Igor V. , Bailone Adriana , Sommer Suzanne , Hübscher Ulrich 
Published: September 2004

SummaryDNA polymerases of the X family have been implicated in a variety of DNA repair processes in eukaryotes. Here we show that Deinococcus radiodurans, a highly radioresistant bacterium able to mend hundreds of radiation‐induced double‐stranded DNA breaks, expresses a DNA polymerase belonging to the X family. This novel bacterial polymerase, named PolXDr, was identified as the product of the Deinococcal DR0467 gene. The purified PolXDr protein possesses a DNA polymerase activity that is stimulated by MnCl2, a property of the X family DNA polymerases. Antibodies raised against PolXDr recognized human pol λ, rat pol β and yeast Pol4 and, conversely, antibodies raised against these proteins recognized PolXDr. This immunological cross‐reactivity suggests a high degree of structural conservation among the polymerases of the X family. Lack of PolXDr reduced the rate of repair of double‐stranded DNA breaks and increased cell sensitivity to γ‐rays. PolXDr thus appears to play an important role in double‐stranded DNA break repair in D. radiodurans.
Subcellular sites for bacterial protein export
Authors: Campo Nathalie , Tjalsma Harold , Buist Girbe , Stepniak Dariusz , Meijer Michel , Veenhuis Marten , Westermann Martin , Müller Jörg P. , Bron Sierd , Kok Jan , Kuipers Oscar P. , Jongbloed Jan D. H. 
Published: September 2004

SummaryMost bacterial proteins destined to leave the cytoplasm are exported to extracellular compartments or imported into the cytoplasmic membrane via the highly conserved SecA‐YEG pathway. In the present studies, the subcellular distributions of core components of this pathway, SecA and SecY, and of the secretory protein pre‐AmyQ, were analysed using green fluorescent protein fusions, immunostaining and/or immunogold labelling techniques. It is shown that SecA, SecY and (pre‐)AmyQ are located at specific sites near and/or in the cytoplasmic membrane of Bacillus subtilis. The localization patterns of these proteins suggest that the Sec machinery is organized in spiral‐like structures along the cell, with most of the translocases organized in specific clusters along these structures. However, this localization appears to be independent of the helicoidal structures formed by the actin‐like cytoskeletal proteins, MreB or Mbl. Interestingly, the specific localization of SecA is dynamic, and depends on active translation. Moreover, reducing the phosphatidylglycerol phospholipids content in the bacterial membrane results in delocalization of SecA, suggesting the involvement of membrane phospholipids in the localization process. These data show for the first time that, in contrast to the recently reported uni‐ExPortal site in the coccoïd Streptococcus pyogenes, multiple sites dedicated to protein export are present in the cytoplasmic membrane of rod‐shaped B. subtilis.
Regulation of root anaerobiosis and carbon translocation by light and root aeration in Isoetes alpinus
Authors: SORRELL B. K. 
Published: September 2004

ABSTRACTThe activity of alcohol dehydrogenase (ADH) was measured in corms and roots of the submerged freshwater macrophyte Isoetes alpinus Kirk. growing in situ, and related to its capacity for internal oxygen transport and to carbohydrate translocation. ADH activity was present in roots but not corms at uniform activity (0.15–0.35 × 10−6 mol  g−1 fresh weight s−1) over the entire plant depth range (3–7 m depth), and was intermediate to that developed in excised roots after 1‐week exposure to either dissolved oxygen at air‐saturation or to anoxia. Responses of photosynthesis and root oxygen release to light intensity confirmed that shoot‐to‐root oxygen transport saturated at similar light intensities to photosynthetic oxygen evolution, but was positive in the dark and at irradiances below the compensation point for photosynthesis, due to contributions to transport by oxygen diffusion from the external medium. Transport of 14C‐labelled photo‐assimilates to roots nevertheless ceased when intact plants were exposed to a combination of leaf darkness and root external anoxia, even when high 14C concentrations were present in shoots, but remained high when the roots were provided with external oxygen. The lack of any control over permeability of the root surface to gases in this species suggested that ADH activity and reduced translocation is most likely caused by development of hypoxic tissues in the apical tissue. These results suggest that reductions in ambient light intensity may have indirect effects on I. alpinus viability by increasing the degree of root hypoxia and impairing carbon partitioning.
Accumulation of pathogenesis‐related (PR) 10/Bet v 1 protein homologues in mulberry (Morus bombycis Koidz.) tree during winter
Authors: UKAJI N. , KUWABARA C. , TAKEZAWA D. , ARAKAWA K. , FUJIKAWA S. 
Published: September 2004

ABSTRACTSeasonal evaluation of total soluble protein fractions extracted from cortical parenchyma cells of mulberry (Morus bombycis Koidz.) tree identified a predominant 18 kDa protein that was directly correlated to periods of cold acclimation. The 18 kDa protein, designated as WAP18 (winter accumulating 18 kDa proteins) increased from September to December and then gradually decreased until June. The maximum levels of WAP18 were detected in mid‐winter, which corresponds to the maximum freeze tolerance in cortical parenchyma cells of mulberry tree. Two‐dimensional gel electrophoresis confirmed that WAP18 consists of at least three proteins that range between an isoelectric point of 5.0 and 6.0. All three proteins reacted with anti‐WAP18 antibodies, thereby suggesting that they represent individual isoforms. Furthermore, N‐terminal amino acid sequence analysis demonstrated that all three proteins contain high sequence similarity to each other and high homology to pathogenesis‐related (PR) −10/Bet v 1 protein families. The purified WAP18 exhibited in vitro cryoprotective activity for the freeze labile l‐lactate dehydrogenase (LDH) enzyme. These results suggest that WAP18 may function in the freezing tolerance mechanism of cortical parenchyma cells of mulberry tree during winter.
Cadmium‐induced subcellular accumulation of O2·− and H2O2 in pea leaves
Authors: ROMERO‐PUERTAS M. C. , RODRÍGUEZ‐SERRANO M. , CORPAS F. J. , GÓMEZ M. , DEL RÍO L. A. , SANDALIO L. M. 
Published: September 2004

ABSTRACTCadmium is a toxic metal that produces disturbances in plant antioxidant defences giving rise to oxidative stress. The effect of this metal on H2O2 and O2·− production was studied in leaves from pea plants growth for 2 weeks with 50 µm Cd, by histochemistry with diaminobenzidine (DAB) and nitroblue tetrazolium (NBT), respectively. The subcellular localization of these reactive oxygen species (ROS) was studied by cytochemistry with CeCl3 and Mn/DAB staining for H2O2 and O2·−, respectively, followed by electron microscopy observation. In leaves from pea plants grown with 50 µm CdCl2 a rise of six times in the H2O2 content took place in comparison with control plants, and the accumulation of H2O2 was observed mainly in the plasma membrane of transfer, mesophyll and epidermal cells, as well as in the tonoplast of bundle sheath cells. In mesophyll cells a small accumulation of H2O2 was observed in mitochondria and peroxisomes. Experiments with inhibitors suggested that the main source of H2O2 could be a NADPH oxidase. The subcellular localization of O2·− production was demonstrated in the tonoplast of bundle sheath cells, and plasma membrane from mesophyll cells. The Cd‐induced production of the ROS, H2O2 and O2·−, could be attributed to the phytotoxic effect of Cd, but lower levels of ROS could function as signal molecules in the induction of defence genes against Cd toxicity. Treatment of leaves from Cd‐grown plants with different effectors and inhibitors showed that ROS production was regulated by different processes involving protein phosphatases, Ca2+ channels, and cGMP.
Inhibition of photosynthesis by high temperature in oak (Quercus pubescensL.) leaves grown under natural conditions closely correlates with a reversible heat‐dependent reduction of the activation state of ribulose‐1,5‐bisphosphate carboxylase/oxygenase
Authors: HALDIMANN P. , FELLER U. 
Published: September 2004

ABSTRACTInhibition of the net photosynthetic CO2assimilation rate (Pn) by high temperature was examined in oak (Quercus pubescensL.) leaves grown under natural conditions. Combined measurements of gas exchange and chlorophyll (Chl)afluorescence were employed to differentiate between inhibition originating from heat effects on components of the thylakoid membranes and that resulting from effects on photosynthetic carbon metabolism. Regardless of whether temperature was increased rapidly or gradually,Pndecreased with increasing leaf temperature and was more than 90% reduced at 45 °C as compared to 25 °C. Inhibition ofPnby heat stress did not result from reduced stomatal conductance (gs), as heat‐induced reduction ofgswas accompanied by an increase of the intercellular CO2concentration (Ci). Chl afluorescence measurements revealed that between 25 and 45 °C heat‐dependent alterations of thylakoid‐associated processes contributed only marginally, if at all, to the inhibition ofPnby heat stress, with photosystem II being remarkably well protected against thermal inactivation. The activation state of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) decreased from about 90% at 25 °C to less than 30% at 45 °C. Heat stress did not affect Rubiscoper se, since full activity could be restored by incubation with CO2and Mg2+. Western‐blot analysis of leaf extracts disclosed the presence of two Rubisco activase polypeptides, but heat stress did not alter the profile of the activase bands. Inhibition ofPnat high leaf temperature could be markedly reduced by artificially increasingCi. A highCialso stimulated photosynthetic electron transport and resulted in reduced non‐photochemical fluorescence quenching. Recovery experiments showed that heat‐dependent inhibition ofPnwas largely, if not fully, reversible. The present results demonstrate that inQ. pubescensleaves the thylakoid membranes in general and photosynthetic electron transport in particular were well protected against heat‐induced perturbations and that inhibition ofPnby high temperature closely correlated with a reversible heat‐dependent reduction of the Rubisco activation state.
Oxidative gating of water channels (aquaporins) in Chara by hydroxyl radicals
Authors: HENZLER T. , YE Q. , STEUDLE E. 
Published: September 2004

ABSTRACTHydroxyl radicals (*OH) as produced in the Fenton reaction (Fe2+ + H2O2 = Fe3+ + OH– + *OH) have been used to reversibly inhibit aquaporins in the plasma membrane of internodes of Chara corallina. Compared to conventional agents such as HgCl2, *OH proved to be more effective in blocking water channels and was less toxic to the cell. When internodes were treated for 30 min, cell hydraulic conductivity (Lp) decreased by 90% or even more. This effect was reversed within a few minutes after removing the radicals from the medium. In contrast to HgCl2, radical treatment reduced membrane permeability of small lipophilic organic solutes (ethanol, acetone, 1‐propanol, and 2‐propanol) by only 24 to 52%, indicating some continued limited movement of these solutes across aquaporins. The biggest effect of *OH treatment on solute permeability was found for isotopic water (HDO), which largely used water channels to cross the membrane. Inhibition of aquaporins reduced the diffusional water permeability (Pd) by about 70%. For the organic test solutes, which mainly use the bilayer to cross the membrane, channel closure caused anomalous (negative) osmosis; that is, cells had negative reflection coefficients (σs) and were transiently swelling in a hypertonic medium. From the ratio of bulk (Lp or osmotic permeability coefficient, Pf) to diffusional (Pd) permeability of water, the number (N) of water molecules that align in water channels was estimated to be N = Pf/Pd = 46 (on average). Radical treatment decreased N from 46 to 11, a value still larger than unity, which would be expected for a membrane lacking pores. The gating of aquaporins by *OH radicals is discussed in terms of a direct action of the radicals when passing the pores or by an indirect action via the bilayer. The rapid recovery of inhibited channels may indicate an easy access of cytoplasmic antioxidants to closed water channels. As hydrogen peroxide is a major signalling substance during different biotic and abiotic stresses, the reversible closure of water channels by *OH (as produced from H2O2 in the apoplast in the presence of transition metals such as Fe2+ or Cu+) may be downstream of the H2O2 signalling. This may provide appropriate adjustments in water relations (hydraulic conductivity), and a common response to different kinds of stresses.
Expression and Characterisation of the Homodimeric E1 Component of the Azotobacter vinelandii Pyruvate Dehydrogenase Complex
Authors: Hengeveld Annechien F. , Westphal Adrie H. , De Kok Aart 
Published: September 2004

We have cloned and sequenced the gene encoding the homodimeric pyruvate dehydrogenase component (Elp) of the pyruvate dehydrogenase complex from Azotobacter vinelandii and expressed and purified the E1p component in Escherichia coli.Cloned E1p can be used to fully reconstitute complex activity. The enzyme was stable in high ionic strength buffers, but was irreversibly inactivated when incubated at high pH, which presumably was caused by its inability to redimerize correctly. This explains the previously found low stability of the wild‐type E1p component after resolution from the complex at high pH.Cloned E1p showed a kinetic behaviour exactly like the wild‐type complex‐bound enzyme with respect to its substrate (pyruvate), its allosteric properties, and its effectors. These experiments show that acetyl coenzyme A acts as a feedback inhibitor by binding to the E1p component.Limited proteolysis experiments showed that the N‐terminal region of E1p was easily removed. The resulting protein fragment was still active with artificial electron acceptors but had lost its ability to bind to the core component (E2p) and thus reconstitute complex activity. E1p was protected against proteolysis by E2p. The allosteric effector pyruvate changed E1p into a conformation that is more resistant to proteolysis.
Modelling ductile fracture behaviour from deformation parameters in HSLA steels
Authors: SIVAPRASAD S. , TARAFDER S. , RANGANATH V. R. , RAY K. K. 
Published: September 2004

ABSTRACTIn this work, an attempt is made to model the ductile fracture behaviour of two Cu‐strengthened high strength low alloy (HSLA) steels through the understanding of their deformation behaviour. The variations in deformation behaviour are imparted by prior deformation of steels to various predetermined strains. The variations in parameters such as yield strength and true uniform elongation with prior deformation is studied and was found to be analogous to that of initiation fracture toughness determined by independent method. A unique method is used to measure the crack tip deformation characterized by stretch zone depth that also depicted a similar trend. Fracture toughness values derived from the stretch zone depth measurements were found to vary in the same fashion as the experimental values. A semiempirical relationship for obtaining ductile fracture toughness from basic deformation parameters is derived and model is demonstrated to estimate initiation ductile fracture toughness accurately.
Diversity of Frankia strains associated to Myrica gale in Western Europe: impact of host plant (Myrica vs. Alnus) and of edaphic factors
Authors: Huguet Valérie , Mergeay Max , Cervantes Emilio , Fernandez Maria P. 
Published: September 2004

SummaryMyricaceae can be nodulated by a variety of Frankia strains isolated from other actinorhizal families. Consequently, the genus Myrica has been considered to have low specificity with respect to microsymbiont taxa. In contrast to controlled studies of Myrica infectious capacity, field studies in North America have indicated that M. gale symbionts belong to the genetic group of Alnus‐infective strains. Myrica gale is the most widely distributed species in the genus so this study focused on describing the genetic diversity of M. gale‐nodulating strains from 10 sites in Western Europe across a range of edaphic conditions. When possible, the specificity of M. gale‐infective strains was compared with that of Alnus‐infective strains from the same sites. Nodular strains from Belgium, France and Spain were characterized using PCR‐RFLP of rrs gene and 16S‐23S IGS. rrs‐RFLP patterns showed a high level of homogeneity among European strains with one dominant genotype. IGS‐RFLP patterns revealed the largest inter and intrasite diversity in France. In Belgium, Frankia strains were found to occur in two groups according to soil pH and organic matter characteristics of the sites. European M. gale‐infective strains were genetically different from European Alnus and North American M. gale‐infective strains indicating the possibility of different pathways of co‐evolution among geographically isolated populations.
Intracellular manganese granules formed by a subsurface bacterium
Authors: Glasauer Susan , Langley Sean , Beveridge Terry J. 
Published: September 2004

SummaryThe demonstrated ability of prokaryotes to form internal metal oxide particles during active metabolism has been restricted to Fe. Mineral‐bound Mn(IV) is a known electron acceptor during dissimilatory metal reduction by Shewanella putrefaciens, yet no internal deposits of Mn have been reported to form during anaerobic respiration. We observed distinct nanometre‐sized Mn‐rich granules in the cytoplasm when either birnessite or pyrolusite (β‐MnO2) served as the electron acceptor during growth. During rapid Mn reduction, additional precipitates of Mn were also observed in the periplasm together with the cytoplasmic granules. The bacteria did not accumulate detectable Mn in the outer membrane during formation of the internal precipitates. This is the first report of an intracellular Mn solid produced by bacteria and coupled anaerobically to DR.
Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms
Authors: Kennedy Nabla , Brodie Eoin , Connolly John , Clipson Nicholas 
Published: September 2004

SummaryA microcosm‐based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved (Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved (Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75‐day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.
Estimating bacterial diversity from clone libraries with flat rank abundance distributions
Authors: Lunn Mary , Sloan William T. , Curtis Thomas P. 
Published: September 2004

SummaryThere are a number of parametric and non‐parametric methods for estimating diversity. However all such methods employ either the proportional abundance of the most abundant taxon in a sample or require that a specific taxon is sampled more than once. Consequently, the available methods for estimating diversity cannot be applied to samples consisting entirely of singletons, which might be characteristic of some hyperdiverse communities. Here we present a non‐parametric method that estimates the probability that a given number of unique taxa would be sampled from a community with a particular diversity. We have applied this approach to a well known data set of 100 unique clones from a sample of Amazonian soil (Borneman and Triplett (1997) Appl Environ Microbiol 63: 2647–2653) and determine the probability that this observation would be made from an environment of a given diversity. On this basis we can state this observation would be very unlikely (P = 0.006) if the soil diversity was less than 103, and quite unlikely (P = 0.6) if the diversity was less than 104, and probable (P = 0.95) if the diversity was about 105. There are essentially no contestable assumptions in our method. Thus we are able to offer almost unequivocal evidence that the bacterial diversity, of at least soils, is very large and a method that may be used to interpret samples consisting entirely of singletons from other hyperdiverse communities.
Illuminating the detection chain of bacterial bioreporters
Authors: Van Der Meer Jan Roelof , Tropel David , Jaspers Marco 
Published: September 2004

SummaryEngineering bacteria for measuring chemicals of environmental or toxicological concern (bioreporter bacteria) has grown slowly into a mature research area. Despite many potential advantages, current bioreporters do not perform well enough to comply with environmental detection standards. Basically, the reasons for this are the lack of engineering principles in the detection chain in the bioreporters. Here, we dissect critical steps in the detection chain and illustrate how bioreporter design could be improved by mutagenizing specificity and selectivity of the sensing and regulatory proteins, by newer expression strategies and application of different signalling networks. Furthermore, we describe how redesigning bioreporter assays with respect to pollutant transport into the cells and application of other detection devices can decrease detection limits and increase the speed of detection.
Foreign Equity Ownership and Information Asymmetry: Evidence from Japan
Authors: Jiang Li , Kim Jeong‐Bon 
Published: September 2004

AbstractUsing a large sample of Japanese firms, we investigate whether the level of foreign ownership in a firm is inversely related to information asymmetry between firm (managers) and market (outside investors). Since information asymmetry is not directly observable and, thus, is difficult to measure empirically, our analysis focuses on the link between foreign shareholding and a measurable consequence of information asymmetry; that is, the timing and magnitude of intertemporal return‐earnings associations. The empirical results support our hypothesis, and subsequent tests based on residual foreign ownership show that the relation between foreign ownership and information asymmetry is robust to the addition of various control variables such as market capitalization and cross‐corporate holdings. We also show that foreign investors tend to avoid stocks with high cross‐corporate holdings. Overall, our results suggest that foreign (institutional) investors are likely to be efficient processors of public information and are attracted to Japanese firms with low information asymmetry.