bluuebunny/crossref_metadata_2025 huggingface dataset:
Current-induced magnetic switching in nanopillar spin-valve systems with double free layers
Authors: Lee Jae-Chul , You Chun-Yeol , Choe Sug-Bong , Lee Kyung-Jin , Shin Kyung-Ho
Published: May 2007

Double soft ferromagnetic layers—CoFe∕Pd∕CoFe—were employed as a free layer of nanopillar spin valve. The system showed double jumps in electric resistance with respect to the spin current. Each jump corresponds to the switching of one of the CoFe layers in the double free layer. The absolute change in resistance of each jump is the same in the resistance versus current scans taken at different applied field values. While both jumps are present only in larger fields, only one jump is observed in low fields, which is attributed to the reversal of the inner CoFe layer. Furthermore, in the latter case an inversion of the hysteresis has been observed, which is explained by telegraph noise.
Density functionals and transition-metal atoms
Authors: Johnson Erin R. , Dickson Ross M. , Becke Axel D.
Published: May 2007

Density-functional calculations on transition-metal atoms are problematic due to the numerous possible ways, having inequivalent densities, of occupying the d orbitals. The problem is compounded by the issue of real orbitals versus complex orbitals. In this work we systematize the application of density-functional theories to transition-metal atoms using a current-density-dependent functional. For all the single-determinantal angular momentum eigenstates of ground-state terms, we obtain near degeneracy for the energies as we should. Also, we find a simple rule for occupying the real d orbitals that reproduces the energies of the (complex) angular momentum eigenstate results. Thus the long-standing confusion over how to compute transition-metal atom reference energies is resolved.
Hydrodynamic interactions between spheres in a viscous fluid with a flat free surface or hard wall
Authors: Cichocki Bogdan , Ekiel-Jeżewska Maria L. , Wajnryb Eligiusz
Published: May 2007

Hydrodynamic interactions between spheres immersed in a low-Reynolds-number fluid flow close to a flat free surface or hard wall are investigated. The spheres may have different or equal radii, and may be separated from the boundary or at contact with the free surface. A simple and useful expression is derived for the propagator (Green operator) connecting centers of two spheres. In the derivation, the method of images and the displacement theorems are used. Symmetry of the displacement operators is explicitly shown. The significance of these results in efficient Stokesian and Brownian dynamics simulations is outlined. An example of an application is shown.
Asymmetrical AlN nanopyramids induced by polar surfaces
Authors: Zheng Jie , Song Xubo , Yu Bo , Li Xingguo
Published: May 2007

Single crystalline wurtzite aluminum nitride (AlN) tetragonal nanopyramids were fabricated through thermal evaporation of aluminum in dilute ammonia flux. The nanopyramids have their tips growing along the [011¯0] direction and exhibit asymmetrical growth behavior along the ±[0001] directions. The formation mechanism was explained by a surface diffusion based model. The observation of the polar surface induced anisotropic growth in AlN nanostructures is expected to provide an insightful sample to investigate the microscopic crystal growth mechanism of AlN and other group III nitrides.
Low density of threading dislocations in AlN grown on sapphire
Authors: Faleev Nikolai , Lu Hai , Schaff William J.
Published: May 2007

We report on high resolution x-ray diffraction studies of the crystalline perfection and the relaxation of elastic strain in AlN grown by MBE on sapphire(0001). Thin (200–300 nm thick) AlN layers were grown with a very low density of threading screw dislocations. A density of 1.75−8.5×105 cm−2, the lowest value ever reported for III-Nitride epitaxial layers, was observed in a surface layer formed over a defective nucleation layer. Residual elastic strain was found in investigated AlN layers. Stress was found to be close to that expected from thermal expansion mismatch between the AlN and sapphire(0001). A model for the structural transformation of crystalline defects accounts for these observations.
Dislocation behavior in KCl crystal under uniaxial compression: Molecular dynamics simulation
Authors: Kinoshita Takahiro , Mashimo Tsutomu , Kawamura Katsuyuki
Published: May 2007

Molecular dynamics simulations of dislocations behavior in KCl crystal under uniaxial compression along the [100], [110], and [111] axis directions were performed to discuss the elastoplastic transition under shock compression. The simulation results showed that the dislocation moved along about 45 deg to the uniaxial compression direction through the displacements of atomic lines around the dislocation core. Under uniaxial compression along the [111] axis direction, two extra half-(011) planes were inserted as dislocations in KCl crystal. The minimum stress for dislocation motion under the uniaxial compression along the [111] axis direction was much larger than those under the uniaxial compressions along the [100] and [110] axis directions. It was suggested that the large minimum stress for dislocation motion along the [111] axis direction was caused by the existence of two edge dislocations which were inserted as extra half-(011) planes. This anisotropic behavior was consistent with the experimental measurement of Hugoniot-elastic limit.
Comment on “Melting dynamics of superheated argon: Nucleation and growth” [J. Chem. Phys. 126, 034505 (2007)]
Authors: Wang L. W.
Published: May 2007

The way to obtain the critical liquid nucleus size N* in the above paper was argued to be not proper with a possibly undoubted and clear method proposed. Furthermore the importance of N* was discussed in view of recent progresses in the mechanism of melting.
High-temperature ferromagnetism in amorphous semiconductor Ge3Mn thin films
Authors: Kim Sung-Kyu , Cho Yong Chan , Jeong Se-Young , Cho Chae-Ryong , Park Sang Eon , Lee J. H. , Kim Jong-Pil , Kim Y. C. , Choi H. W.
Published: May 2007

The Ge1−xMnx thin films were fabricated at x=0.25, of which the composition is close to Ge3Mn. They showed ferromagnetism up to above 350K, even though their structure is amorphous. Ge3Mn amorphous samples grown at 200°C have n-type characteristics, while those grown at 500°C have p-type characteristics. The former has a different state from the latter, energetically. It is suggested that the different short range orders of Ge3Mn5 and/or Ge8Mn11 have already formed in the amorphous phase according to the growth temperature. The authors have also discussed the relationship between ferromagnetism and cluster formations after annealing at 800°C.
Differential tolerance in wheat (Triticum aestivum L.) genotypes to metribuzin
Authors: Kleemann S. G. L. , Gill G. S.
Published: May 2007

Field and glasshouse experiments were undertaken at 2 locations in South Australia to evaluate wheat (Triticum aestivum L.) tolerance to metribuzin. Sloop SA barley (Hordeum vulgare L.) was used as a standard in the evaluation. Linear and logistic regression models were used to describe the response of wheat genotypes to metribuzin. Parameter estimates of B (slope) and ED50 (dose required for 50% inhibition) estimated by the models were used to compare the responses of the genotypes with that of the known sensitive cv. Spear. In the field, wheat cvv. Blade, Kite, EGA Eagle Rock, and Sloop SA barley showed tolerance to metribuzin, exhibiting little change in seedling density and anthesis dry matter (DM) when treated with metribuzin (187.5 and 375 g/ha). In contrast, wheat cv. Spear, which has 50% common parentage with Blade, showed a strong negative response to metribuzin for both seedling density (B = –0.308) and anthesis DM (B = –0.482), indicating sensitivity to the herbicide. Sonora 64 and Tezanos Pinto Precoz, parental lines of Blade, were also sensitive to metribuzin (>187.5 g/ha), showing similar negative responses to that of Spear for anthesis dry matter (B = –0.307 and –0.387). However, Kite, which is another parent of Blade, showed excellent tolerance to this herbicide, exhibiting only a small response (B = –0.076), which was statistically (P < 0.05) different from that of Spear. In the second field study, cvv. Blade, EGA Eagle Rock, and Sloop SA barley were again far more tolerant to metribuzin than the sensitive cv. Spear, requiring almost double the dose of metribuzin to induce 50% inhibition (ED50). Glasshouse studies, where metribuzin was highly active in a light sandy potting soil at what would be considered low rates in the field (50 and 100 g/ha), confirmed the sensitivity differences among wheat genotypes observed in the field. Wheat genotypes Blade, Kite, EGA Eagle Rock, and daughter line RAC 0824 were consistently tolerant to metribuzin. Sensitivity to metribuzin (50 g/ha) was observed in Spear, and most parental lines of Blade with the exception of Kite. Interestingly, Kite showed equivalent tolerance to its progeny, Blade and EGA Eagle Rock, exhibiting similar ED50 and B (slope) values. It is noteworthy that EGA Eagle Rock has recently been specifically bred for tolerance to metribuzin using Blade as a parent. Considering Kite was the only parent to show tolerance to metribuzin in these field and glasshouse studies, it would appear to be the major contributor to metribuzin tolerance in cv. Blade. At present, Kite is not favoured by wheat breeders due to the presence of a rust-resistant gene (SR26) linked to yield penalty. Further research is required to determine alleles responsible for metribuzin tolerance in wheat and to identify alternative sources of metribuzin tolerance.
Changes in seed size and oil accumulation in Brassica napus L. by manipulating the source - sink ratio and excluding light from the developing siliques
Authors: Fortescue Jeanie A. , Turner David W.
Published: May 2007

Most of the oil in canola seed is contained in the cotyledons and so an increase in cotyledon size may lead to increased oil concentration in the whole seed, provided compensatory changes in non-oil bearing tissues are minimised. In addition, in in vitro studies, light has been shown to affect fatty acid synthesis. In two glasshouse experiments, we manipulated seed size in 3 cultivars of canola by increasing the source–sink ratio through removal of lateral inflorescences, restricting the plants to flowering on the main axis. We manipulated the ability of the growing seed to use light for the synthesis of fatty acids for oil by shading the siliques at different stages of seed development. The growth of ovules and embryos in the first experiment was assessed by evaluating changes in the projected area of the organs during growth and the final seed weight. We examined the pattern of organ development in the embryo by fitting appropriate curves and comparing the effect of the treatments on the coefficients.
Pruning axillary branches increased seed weight by 14–43% but did not change the pattern of development of the cotyledons or radicle in the seed. Embryo growth over time was sigmoid in form with the most rapid growth occurring 12–27 days after flowering (daf). The removal of axillary branches and inflorescences reduced oil concentration in the larger seeds by 2.6–4.5% but only in one experiment.
Light was excluded from the siliques from 2, 10, or 30 daf or not at all. Excluding light from 2 or 10 daf reduced ovule weight at maturity by 63% and excluding light from 30 daf reduced ovule weight by 20%. Excluding light reduced the number of seeds per silique by up to 90%, especially when excluded from 2 daf. Excluding light slightly reduced oil concentration, suggesting that, provided maternal substrates are available to the seed, it can use these to obtain energy for oil synthesis, even in the dark. We conclude that manipulation of the canopy of canola to change the source–sink ratio or the distribution of light within the canopy may have large effects on seed size, but little effect on the accumulation of oil in the seeds. This conclusion assumes that the relationships found in our glasshouse experiments apply in the field.
Genetic evaluation of crossbred lamb production. 3. Growth and carcass performance of second-cross lambs
Authors: Afolayan R. A. , Fogarty N. M. , Ingham V. M. , Gilmour A. R. , Gaunt G. M. , Cummins L. J. , Pollard T.
Published: May 2007

This study evaluated the growth and carcass performance of second-cross lambs that were the progeny of common terminal sires and a range of first-cross ewes. The first-cross ewes were the progeny of 91 industry sires from several maternal breeds including the Border Leicester, East Friesian, Finnsheep, Coopworth, White Suffolk, Corriedale, and Booroola Leicester breeds. The first-cross ewes were generated at 3 sites over 3 years, and 3 common maternal sires were used at each site and each year to provide genetic links for combined analysis. The 2726 first-cross ewes were mated naturally to common terminal sires for 3 years at each site to quantify the variation in maternal genetics on the performance of 11 341 second-cross cross lambs. The birthweight, weaning weight (at an average age of 100 days) and post-weaning weight (at an average age of 200 days) of the second-cross lambs were analysed using mixed-model procedures. The lambs were slaughtered (n = 8878) at an average target carcass weight of 22 kg and dressing yield, carcass fat, muscle, meat colour, and meat pH were analysed. Crossbred ewe breed (the maternal grand sire breed) was significant for birthweight (range of 0.9 kg), weaning weight (range 4.4 kg) and post-weaning weight (range 4.6 kg). Type of birth and rearing, age of dam, and sex effects were significant for all liveweights. Ewe breed was significant for hot carcass weight, carcass fat levels, and muscle dimensions, but not for meat colour and ultimate meat pH. There was a significant difference between wether and ewe lamb carcasses for most traits, with other fixed effects generally being small when carcass weight was included as a covariate. Lamb carcasses from East Friesian-cross ewes were very lean compared with carcasses from all other ewe breeds (~2 mm lower fat depth at the GR site at 22 kg carcass weight). This comprehensive study of maternal sire breeds provides an opportunity to exploit between-breed variation for some maternal growth and carcass traits. There was, however, considerable overlap among breeds and opportunities exist for additional improvement by exploiting between-maternal sire genetic variance. The role of improved growth and carcass performance in profitability of prime lamb enterprises is discussed.
MPS3 mediates meiotic bouquet formation in
Saccharomyces cerevisiae
Authors: Conrad Michael N. , Lee Chih-Ying , Wilkerson Joseph L. , Dresser Michael E.
Published: May 2007

In meiotic prophase, telomeres associate with the nuclear envelope and accumulate adjacent to the centrosome/spindle pole to form the chromosome bouquet, a well conserved event that in
Saccharomyces cerevisiae
requires the meiotic telomere protein Ndj1p. Ndj1p interacts with Mps3p, a nuclear envelope SUN domain protein that is required for spindle pole body duplication and for sister chromatid cohesion. Removal of the Ndj1p-interaction domain from
MPS3
creates an
ndj1
Δ-like separation-of-function allele, and Ndj1p and Mps3p are codependent for stable association with the telomeres. SUN domain proteins are found in the nuclear envelope across phyla and are implicated in mediating interactions between the interior of the nucleus and the cytoskeleton. Our observations indicate a general mechanism for meiotic telomere movements.
The tumor suppressor
CYLD
regulates entry into mitosis
Authors: Stegmeier Frank , Sowa Mathew E. , Nalepa Grzegorz , Gygi Steven P. , Harper J. Wade , Elledge Stephen J.
Published: May 2007

Mutations in the cylindromatosis (
CYLD
) gene cause benign tumors of skin appendages, referred to as cylindromas. The
CYLD
gene encodes a deubiquitinating enzyme that removes Lys-63-linked ubiquitin chains from IκB kinase signaling components and thereby inhibits NF-κB pathway activation. The dysregulation of NF-κB activity has been proposed to promote cell transformation in part by increasing apoptosis resistance, but it is not clear whether this is
CYLD
's only or predominant tumor-suppressing function. Here, we show that
CYLD
is also required for timely entry into mitosis. Consistent with a cell-cycle regulatory function,
CYLD
localizes to microtubules in interphase and the midbody during telophase, and its protein levels decrease as cells exit from mitosis. We identified the protein kinase Plk1 as a potential target of
CYLD
in the regulation of mitotic entry, based on their physical interaction and similar loss-of-function and overexpression phenotypes. Our findings raise the possibility that, as with other genes regulating tumorigenesis,
CYLD
has not only tumor-suppressing (apoptosis regulation) but also tumor-promoting activities (enhancer of mitotic entry). We propose that this additional function of
CYLD
could provide an explanation for the benign nature of most cylindroma lesions.
Derivation of site-specific skeletal masses within the current ICRP age series
Authors: Watchman Christopher J , Hasenauer Deanna , Bolch Wesley E
Published: May 2007

The calculation of absorbed dose to the radiosensitive tissues of the skeleton is routinely performed using reference masses provided in publications from the International Commission on Radiological Protection (ICRP). These values typically include total skeleton tissue masses by reference subject age, but not by individual bone site at a given age. Site-specific variations in absorbed fractions are known to occur for internal alpha-particle and beta-particle emitters, and in certain medical dose reconstructions, site-specific estimates of marrow dose may be desirable. Furthermore, bone-site-specific tissue masses are required to properly estimate skeletal-averaged absorbed fractions and, more importantly, specific absorbed fractions for internalized radionuclides and radiopharmaceuticals. Reference masses by skeletal site are also needed in the development of ICRP compliant tomographic phantoms, as this organ system is initially segmented from medical images only as a homogeneous tissue region. ICRP reference skeletal masses are assigned based upon several independent data sources, many of which may not be entirely consistent with one another. In this study, a methodology is presented, using data from the various ICRP publications, to derive site-specific skeletal tissue masses for each member of the ICRP age series. Active marrow masses are calculated and differences are shown with respect to ICRP Publications 70 and 89 values. New data for a revised surrogate tissue region for the osteoprogenitor cells within bone marrow is presented with estimates of its total mass throughout the skeleton and for different subject ages.
Sugar Import and Phytopathogenicity ofSpiroplasma citri: Glucose and Fructose Play Distinct Roles
Authors: André Aurélie , Maucourt Mickaël , Moing Annick , Rolin Dominique , Renaudin Joël
Published: May 2007

We have shown previously that the glucose PTS (phos-photransferase system) permease enzyme II of Spiroplasma citri is split into two distinct polypeptides, which are encoded by two separate genes, crr and ptsG. A S. citri mutant was obtained by disruption of ptsG through homologous recombination and was proved unable to import glucose. The ptsG mutant (GII3-glc1) was transmitted to periwinkle (Catharanthus roseus) plants through injection to the leaf-hopper vector. In contrast to the previously characterized fructose operon mutant GMT 553, which was found virtually nonpathogenic, the ptsG mutant GII3-glc1 induced severe symptoms similar to those induced by the wild-type strain GII-3. These results, indicating that fructose and glucose utilization were not equally involved in pathogenicity, were consistent with biochemical data showing that, in the presence of both sugars, S. citri used fructose preferentially. Proton nuclear magnetic resonance analyses of carbohydrates in plant extracts revealed the accumulation of soluble sugars, particularly glucose, in plants infected by S. citri GII-3 or GII3-glc1 but not in those infected by GMT 553. From these data, a hypothetical model was proposed to establish the relationship between fructose utilization by the spiroplasmas present in the phloem sieve tubes and glucose accumulation in the leaves of S. citri infected plants.
Identification of cis-Active Elements in Ustilago maydis mig2 Promoters Conferring High-Level Activity During Pathogenic Growth in Maize
Authors: Farfsing Jan W. , Auffarth Kathrin , Basse Christoph W.
Published: May 2007

The Ustilago maydis mig2 cluster comprises five highly homologous genes that display a pronounced plant-specific expression profile. A 350-bp mig2-5 promoter fragment contained all elements sufficient to confer differential promoter activity. Mutational analysis of this region, fused to the green fluorescent protein reporter gene, allowed dissecting core promoter elements required for high-level promoter activity from elements conferring inducible expression in planta. In particular, the presence of several 5′-CCA-3′ motifs within a short stretch of the mig2-5 promoter was decisive for inducible promoter activity. On this basis, we reconstituted an artificial promoter whose inducible activity specifically relied on multiple CCA motifs. In addition, we identified a novel mig2 homologous gene, mig2-6, that is not part of the mig2 cluster, but displayed the strongest differential expression profile among mig2 genes. The deletion of all six mig2 genes did not compromise the ability to induce tumor formation in infected maize plants. Comparative sequence analysis including the mig2-6 promoter revealed an over-representation of the consensus motif 5′-MNMNWNCCAMM-3′. We discuss putative transcriptional activators involved in mig2 regulation.
Diversification of Non-TIR Class NB-LRR Genes in Relation to Whole-Genome Duplication Events in Arabidopsis
Authors: Nobuta Kan , Ashfield Tom , Kim Sun , Innes Roger W.
Published: May 2007

Arabidopsis thaliana is believed to have experienced at least two and possibly three whole-genome duplication events in its evolutionary history. In order to investigate the evolutionary relationships between these duplication events and diversification of disease resistance (R) genes, segmental-duplication events containing R genes belonging to the nucleotide binding-leucine rich repeat (NB-LRR) class were identified. Of 153 segmental-duplication events containing NB-LRR genes, only 22 contained NB-LRR genes in both members of the duplication pair, indicating a high frequency of NB-LRR gene loss after wholegenome duplication. The relative age of the duplication events was estimated based on the average synonymous substitution rate of the duplicated gene pairs in the segments. These data were combined with phylogenetic analyses. NB-LRR genes present in segment pairs derived from the most recent whole-genome duplication event, estimated to have occurred only 20 to 40 million years ago, occupy very distant branches of the NB-LRR phylogenetic tree. These data suggest that when NB-LRR clusters are duplicated as part of a whole-genome duplication, homoeologous NB-LRR genes are preferentially lost, either by eliminating one copy of the cluster or by eliminating individual genes such that only paralogous NB-LRR genes are maintained.
Mutations of ousA Alter the Virulence of Erwinia chrysanthemi
Authors: Gloux Karine , Touze Thierry , Pagot Yves , Jouan Bernard , Blanco Carlos
Published: May 2007

A negative correlation was observed between the aggressiveness of several Erwinia chrysanthemi strains on potato tuber and their osmotic tolerance. The disruption of the ousA gene encoding the major osmoprotectant uptake system highly enhanced bacterial virulence on potato tubers. The ousA disruption also increased the maceration efficiency on potato tubers under anaerobic conditions. In the absence of oxygen, pectate lyase (Pel) production was significantly higher in the tissue macerated with the ousA- strain than with the wild type. Oxygen content is significantly different between infected and healthy tissues; therefore, ousA may be a contributory factor in the infection progression within the host. In minimal medium, ousA disruption enhanced Pel production and pelE expression only under micro-aerobiosis conditions. The effect on Pel was reversed by reintroduction of the ousA gene. The osmoprotectectants glycine betaine, proline betaine, and pipecolic acid are known to be taken up via OusA and to have an inhibitory effect on Pel production. However, their effects on Pel activity were not (glycine betaine) or only weakly (proline and pipecolic acid) affected by ousA disruption. Furthermore, no correlation was observed between their effects on Pel activities and their osmoprotection efficacies. The results demonstrate a relationship between E. chrysanthemi pathogenicity factors and the activity of ousA under low oxygen status. The evidence indicates that ousA and osmoprotectant effects on Pel are not linked to osmoregulation and that complex regulations exist between Pel production, ousA, and osmoprotection via compounds liberated during the plant infection.
Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi
Authors: Randall Thomas A. , Dwyer Rex A. , Huitema Edgar , Beyer Katinka , Cvitanich Cristina , Kelkar Hemant , Ah Fong Audrey M. V. , Gates Krista , Roberts Samuel , Yatzkan Einat , Gaffney Thomas , Law Marcus , Testa Antonino , Torto-Alalibo Trudy , Zhang Meng , Zheng Li , Mueller Elisabeth , Windass John , Binder Andres , Birch Paul R. J. , Gisi Ulrich , Govers Francine , Gow Neil A. , Mauch Felix , van West Pieter , Waugh Mark E. , Yu Jun , Boller Thomas , Kamoun Sophien , Lam Stephen T. , Judelson Howard S.
Published: May 2007

To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coveragethe P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.
The Pseudomonas chlororaphis PCL1391 Sigma Regulator psrA Represses the Production of the Antifungal Metabolite Phenazine-1-Carboxamide
Authors: Chin-A-Woeng Thomas F. C. , van den Broek Daan , Lugtenberg Ben J. J. , Bloemberg Guido V.
Published: May 2007

The rhizobacterium Pseudomonas chlororaphis PCL1391 produces the antifungal metabolite phenazine-1-carboxamide (PCN), which is a crucial trait in its competition with the phytopathogenic fungus Fusarium oxysporum f. sp. radicis-lycopersici in the rhizosphere. The expression of the PCN biosynthetic gene cluster in PCL1391 is population density-dependent and is regulated by the quorum-sensing genes phzI and phzR via synthesis of the autoinducer Nhexanoyl-L-homoserine lactone (C6-HSL). Here, we describe the identification of an additional regulatory gene of PCN biosynthesis in PCL1391. A mutation in the psrA gene (Pseudomonas sigma regulator), the gene product of which is a member of the TetR/AcrR family of transcriptional regulators, resulted in increased production of autoinducer molecules and PCN. Expression studies showed that inactivation of psrA resulted in increased expression of the phzI and phzR genes and the phz biosynthetic operon and that introduction of functional copies of psrA represses the expression of these genes, resulting in reduced production of autoinducer signal and PCN. Surprisingly, inactivation of psrA in the phzI or phzR quorum-sensing mutants, which do not produce detectable amounts of PCN and autoinducers by themselves, restored PCN biosynthesis. This phenomenon was accompanied by the appearance of compounds with autoinducer activities migrating at the positions of C4-HSL and C6-HSL on C18 reverse phase-thin-layer chromatography. These observations indicate that PsrA also represses at least one silent, yet unidentified, quorum-sensing system or autoinducer biosynthetic pathway in PCL1391. The expression of psrA declines at the onset of the stationary phase at the same moment at which quorum-sensing (-regulated) genes are activated. In addition, expression studies in a psrA- and a multicopy psrA background showed that psrA is autoregulated. Multiple copies of psrA repress its own expression. Mutation of gacS, encoding the sensor kinase member of a two-component global regulatory system significantly reduced production of autoinducers and PCN. We show a novel link between global regulation and quorum sensing via the PsrA regulator.
RpoN (σ54) Controls Production of Antifungal Compounds and Biocontrol Activity in Pseudomonas fluorescens CHA0
Authors: Péchy-Tarr Maria , Bottiglieri Mélanie , Mathys Sophie , Lejbølle Kirsten Bang , Schnider-Keel Ursula , Maurhofer Monika , Keel Christoph
Published: May 2007

Pseudomonas fluorescens CHA0 is an effective biocontrol agent of root diseases caused by fungal pathogens. The strain produces the antibiotics 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin (PLT) that make essential contributions to pathogen suppression. This study focused on the role of the sigma factor RpoN (σ54) in regulation of antibiotic production and biocontrol activity in P. fluorescens. An rpoN in-frame-deletion mutant of CHA0 had a delayed growth, was impaired in the utilization of several carbon and nitrogen sources, and was more sensitive to salt stress. The rpoN mutant was defective for flagella and displayed drastically reduced swimming and swarming motilities. Interestingly, the rpoN mutant showed a severalfold enhanced production of DAPG and expression of the biosynthetic gene phlA compared with the wild type and the mutant complemented with monocopy rpoN+. By contrast, loss of RpoN function resulted in markedly lowered PLT production and plt gene expression, suggesting that RpoN controls the balance of the two antibiotics in strain CHA0. In natural soil microcosms, the rpoN mutant was less effective in protecting cucumber from a root rot caused by Pythium ultimum. Remarkably, the mutant was not significantly impaired in its root colonization capacity, even at early stages of root infection by Pythium spp. Taken together, our results establish RpoN for the first time as a major regulator of biocontrol activity in Pseudomonas fluorescens.
Tomato Defense to Oldium neolycopersici: Dominant OI Genes Confer Isolate-Dependent Resistance Via a Different Mechanism Than Recessive oI-2
Authors: Bai Yuling , van der Hulst Ron , Bonnema Guusje , Marcel Thierry C. , Meijer-Dekens Fien , Niks Rients E. , Lindhout Pim
Published: May 2007

Tomato powdery mildew caused by Oidium neolycopersici has become a globally important disease of tomato (Lycopersicon esculentum). To study the defense responses of tomato triggered by tomato powdery mildew, we first mapped a set of resistance genes to O. neolycopersici from related Lycopersicon species. An integrated genetic map was generated showing that all the dominant resistance genes (Ol-1, Ol-3, Ol-4, Ol-5, and Ol-6) are located on tomato chromosome 6 and are organized in three genetic loci. Then, near-isogenic lines (NIL) were produced that contain the different dominant Ol genes in a L. esculentum genetic background. These NIL were used in disease tests with local isolates of O. neolycopersici in different geographic locations, demonstrating that the resistance conferred by different Ol genes was isolate-dependent and, hence, may be race-specific. In addition, the resistance mechanism was analyzed histologically. The mechanism of resistance conferred by the dominant Ol genes was associated with hypersensitive respo-nse, which varies in details depending on the Ol-gene in the NIL, while the mechanism of resistance governed by the recessive gene ol-2 on tomato chromosome 4 was associated with papillae formation.
Arabidopsis ssi2-Conferred Susceptibility to Botrytis cinerea Is Dependent on EDS5 and PAD4
Authors: Nandi Ashis , Moeder Wolfgang , Kachroo Pradeep , Klessig Daniel F. , Shah Jyoti
Published: May 2007

Loss of a stearoyl-ACP desaturase activity in the Arabidopsis thaliana ssi2 mutant confers susceptibility to the necrotroph, Botrytis cinerea. In contrast, the ssi2 mutant exhibits enhanced resistance to Pseudomonas syringae, Peronospora parasitica, and Cucumber mosaic virus. The altered basal resistance to these pathogens in the ssi2 mutant plant is accompanied by the constitutive accumulation of elevated salicylic acid (SA) level and expression of the pathogenesis-related 1 (PR1) gene, the inability of jasmonic acid (JA) to activate expression of the defensin gene, PDF1.2, and the spontaneous death of cells. Here, we show that presence of the eds5 and pad4 mutant alleles compromises the ssi2-conferred resistance to Pseudomonas syringae pv. maculicola. In contrast, resistance to B. cinerea was restored in the ssi2 eds5 and ssi2 pad4 double-mutant plants. However, resistance to B. cinerea was not accompanied by the restoration of JA responsiveness in the ssi2 eds5 and ssi2 pad4 plants. The ssi2 eds5 and ssi2 pad4 plants retain the ssi2-conferred spontaneous cell death phenotype, suggesting that cell death is not a major factor that predisposes the ssi2 mutant to infection by B. cinerea. Furthermore, the high SA content of the ssi2 pad4 plant, combined with our previous observation that the SA-deficient ssi2 nahG plant succumbs to infection by B. cinerea, suggests that elevated SA level does not have a causal role in the ssi2-conferred susceptibility to B. cinerea. Our results suggest that interaction between an SSI2-dependent factor or factors and an EDS5- and PAD4- dependent mechanism or mechanisms modulates defense to B. cinerea.
RAR1, ROR1, and the Actin Cytoskeleton Contribute to Basal Resistance to Magnaporthe grisea in Barley
Authors: Jarosch Birgit , Collins Nicholas C. , Zellerhoff Nina , Schaffrath Ulrich
Published: May 2007

The fungus Magnaporthe grisea, the causal agent of rice blast disease, is a major pathogen of rice and is capable of producing epidemics on other cultivated cereals, including barley (Hordeum vulgare). We explored the requirements for basal resistance of barley against a compatible M. grisea isolate using both genetic and chemical approaches. Mutants of the RAR1 gene required for the function of major resistance gene-mediated resistance and mutants of the ROR1 and ROR2 genes required for full expression of cell-wall-penetration resistance against powdery mildew pathogens were examined for macroscopic and microscopic alterations in M. grisea growth and symptoms. RAR1 contributed to resistance in epidermis and mesophyll at different stages of fungal infection dependent on the MLO/mlo-5 status. Whereas no ROR2 effect was detected, ROR1 was found to contribute to cell-wall-penetration resistance, at least in the epidermis. Application of the actin agonist cytochalasin E promoted cell wall penetration by M. grisea in a dose-dependent manner, demonstrating an involvement of the actin cytoskeleton in penetration resistance.
Comparison of the Transcript Profiles from the Root and the Nodulating Root of the Model Legume Lotus japonicus by Serial Analysis of Gene Expression
Authors: Asamizu Erika , Nakamura Yasukazu , Sato Shusei , Tabata Satoshi
Published: May 2007

We performed a comprehensive transcript analysis on the early stage of root nodulation in the model legume Lotus japonicus by serial analysis of gene expression (SAGE). SAGE libraries were made from uninfected roots and nodulating roots abundant in nodule primordia, and 85,482 and 80,233 SAGE tags were recovered, respectively. Comparison of the tag frequency identified 407 tag species that appeared in significantly greater numbers in the nodulating root than in the uninfected root, and the converse was found for 428 tag species. Gene identification of the tags was performed by matching them to L. japonicus expressed sequence tag sequences. We made several novel findings by applying SAGE to transcript analysis of legume root nodulation. A gene that showed the most significant increase in tag number upon nodulation has not been described previously. Different levels of transcription induction among leghemoglobin gene paralogs were found, indicating the effectiveness of SAGE in discriminating different gene family members. We identified genes for 44 unknown tags by means of reverse SAGE. We found 11 antisense tags that increased during nodulation, indicating that regulation of gene expression by antisense transcripts may occur in an organ-dependent manner.
Overexpression of a Rice NPR1 Homolog Leads to Constitutive Activation of Defense Response and Hypersensitivity to Light
Authors: Chern Mawsheng , Fitzgerald Heather A. , Canlas Patrick E. , Navarre Duroy A. , Ronald Pamela C.
Published: May 2007

Arabidopsis NPR1/NIM1 is a key regulator of systemic acquired resistance (SAR), which confers lasting broad-spectrum resistance. Previous reports indicate that rice has a disease-resistance pathway similar to the Arabidopsis SAR pathway. Here we report the isolation and characterization of a rice NPR1 homologue (NH1). Transgenic rice plants overexpressing NH1 (NH1ox) acquire high levels of resistance to Xanthomonas oryzae pv. oryzae. The resistance phenotype is heritable and correlates with the presence of the transgene and reduced bacterial growth. Northern analysis shows that NH1ox rice spontaneously activates defense genes, contrasting with NPR1-overexpressing Arabidopsis, where defense genes are not activated until induction. Wild-type NH1, but not a point mutant corresponding to npr1-1, interacts strongly with the rice transcription factor rTGA2.2 in yeast two-hybrid. Greenhouse-grown NH1ox plants develop lesion-mimic spots on leaves at preflowering stage although no other developmental effects are observed. However, when grown in growth chambers (GCs) under low light, NH1ox plants are dwarfed, indicating elevated sensitivity to light. The GC-grown NH1ox plants show much higher salicylic acid (SA) levels than the wild type, whereas greenhouse-grown NH1ox plants contain lower SA. These results indicate that NH1 may be involved in the regulation of SA in response to environmental changes.
Characterization of the hrpF Pathogenicity Peninsula of Xanthomonas oryzae pv. oryzae
Authors: Sugio Akiko , Yang Bing , White Frank F.
Published: May 2007

The hrp gene cluster of Xanthomonas spp. contains genes for the assembly and function of a type III secretion system (TTSS). The hrpF genes reside in a region between hpaB and the right end of the hrp cluster. The region of the hrpF gene of Xanthomonas oryzae pv. oryzae is bounded by two IS elements and also contains a homolog of hpaF of X. campestris pv. vesicatoria and two newly identified genes, hpa3 and hpa4. A comparison of the hrp gene clusters of different species of Xanthomonas revealed that the hrpF region is a constant yet more variable peninsula of the hrp pathogenicity island. Mutations in hpaF, hpa3, and hpa4 had no effect on virulence, whereas hrpF mutants were severely reduced in virulence on susceptible rice cultivars. The hrpF genes from X. campestris pv. vesicatoria, X. campestris pv. campestris, and X. axonopodis pv. citri each were capable of restoring virulence to the hrpF mutant of X. oryzae pv. oryzae. Correspondingly, none of the Xanthomonas pathovars with hrpF from X. oryzae pv. oryzae elicited a hypersensitive reaction in their respective hosts. Therefore, no evidence was found for hrpF as a host-specialization factor. In contrast to the loss of Bs3-dependent reactions by hrpF mutants of X. campestris pv. vesicatoria, hrpF mutants of X. oryzae pv. oryzae with either avrXa10 or avrXa7 elicited hypersensitive reactions in rice cultivars with the corresponding R genes. A double hrpFxoo-hpa1 mutant also elicited an Xa10-dependent resistance reaction. Thus, loss of hrpF, hpa1, or both may reduce delivery or effectiveness of type III effectors. However, the mutations did not completely prevent the delivery of effectors from X. oryzae pv. oryzae into the host cells.
Isolation of an N-alkylated Benzylamine Derivative from Pseudomonas putida BTP1 as Elicitor of Induced Systemic Resistance in Bean
Authors: Ongena Marc , Jourdan Emmanuel , Schäfer Mathias , Kech Cécile , Budzikiewicz Herbert , Luxen André , Thonart Philippe
Published: May 2007

Root treatment of Phaseolus vulgaris with the nonpathogenic Pseudomonas putida BTP1 led to significant reduction of the disease caused by the pathogen Botrytis cinerea on leaves. The molecular determinant of P. putida BTP1 mainly responsible for the induced systemic resistance (ISR) was isolated from cell-free culture fluid after growth of the strain in the iron-poor casamino acid medium. Mass spectrometry analyses performed on both the bacterial product and synthetic analogues revealed a polyalkylated benzylamine structure, with the quaternary ammonium substituted by methyl, ethyl, and C13 aliphatic groups responsible for the relative hydrophobicity of the molecule. The specific involvement of the N-alkylated benzylamine derivative (NABD) in ISR elicitation was first evidenced by testing the purified compound that mimicked the protective effect afforded by crude supernatant samples. The evidence was supported by the loss of elicitor activity of mutants impaired in NABD biosynthesis. Our experiments also showed that other iron-regulated metabolites secreted by the strain are not involved in ISR stimulation. Thus, these results indicate a wider variety of Pseudomonas determinants for ISR than reported to date.
Application of RNA Interference to Root-Knot Nematode Genes Encoding Esophageal Gland Proteins
Authors: Rosso M.-N. , Dubrana M. P. , Cimbolini N. , Jaubert S. , Abad P.
Published: May 2007

Plant parasitic nematodes have been, so far, refractory to transformation or mutagenesis. The functional analysis of nematode genes relies on the development of reverse genetic tools adapted to these obligate parasites. Here, we describe the application of RNA interference (RNAi) to the root-knot nematode Meloidogyne incognita for the knock-down of two genes expressed in the subventral esophageal glands of the nematode and potentially involved in parasitism, the calreticulin (Mi-crt) and the polygalacturonase (Mi-pg-1) genes. Incubation in 1% resorcinol for 4 h induced double-stranded RNA uptake through the alimentary track of the nematodes and led to up to 92% depletion of Mi-crt transcripts. Timecourse analysis of the silencing showed different temporal patterns for Mi-crt and Mi-pg-1. The silencing of Mi-crt was optimal 20 h after soaking, whereas the silencing of Mi-pg-1 was optimal 44 h after soaking. For the two genes, the silencing effect was highly time-limited, since no transcript depletion was detectable 68 h after soaking.
Role of Trehalose Transport and Utilization in Sinorhizobium meliloti-Alfalfa Interactions
Authors: Jensen John Beck , Ampomah Osei Yaw , Darrah Richard , Peters N. Kent , Bhuvaneswari T. V.
Published: May 2007

Genes thuA and thuB in Sinorhizobium meliloti Rm1021 code for a major pathway for trehalose catabolism and are induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. S. meliloti strains mutated in either of these two genes were severely impaired in their ability to grow on trehalose as the sole source of carbon. ThuA and ThuB show no homology to any known enzymes in trehalose utilization. ThuA has similarity to proteins of unknown function in Mesorhizobium loti, Agrobacterium tumefaciens, and Brucella melitensis, and ThuB possesses homology to dehydrogenases containing the consensus motif AGKHVXCEKP. thuAB genes are expressed in bacteria growing on the root surface and in the infection threads but not in the symbiotic zone of the nodules. Even though thuA and thuB mutants were impaired in competitive colonization of Medicago sativa roots, these strains were more competitive than the wild-type Rm1021 in infecting alfalfa roots and forming nitrogen-fixing nodules. Possible reasons for their increased competitiveness are discussed.
The Late Blight Resistance Locus Rpi-blb3 from Solanum bulbocastanum Belongs to a Major Late Blight R Gene Cluster on Chromosome 4 of Potato
Authors: Park Tae-Ho , Gros Jack , Sikkema Anne , Vleeshouwers Vivianne G. A. A. , Muskens Marielle , Allefs Sjefke , Jacobsen Evert , Visser Richard G. F. , van der Vossen Edwin A. G.
Published: May 2007

Late blight, caused by Phytophthora infestans, is one of the most devastating diseases in cultivated potato. Breeding of new potato cultivars with high levels of resistance to P. infestans is considered the most durable strategy for future potato cultivation. In this study, we report the identification of a new late-blight resistance (R) locus from the wild potato species Solanum bulbocastanum. Using several different approaches, a high-resolution genetic map of the new locus was generated, delimiting Rpi-blb3 to a 0.93 cM interval on chromosome 4. One amplification fragment length polymorphism marker was identified that cosegregated in 1,396 progeny plants of an intraspecific mapping population with Rpi-blb3. For comparative genomics purposes, markers linked to Rpi-blb3 were tested in mapping populations used to map the three other late-blight R loci Rpi-abpt, R2, and R2-like also to chromosome 4. Marker order and allelic conservation suggest that Rpi-blb3, Rpiabpt, R2, and R2-like reside in the same R gene cluster on chromosome 4 and likely belong to the same gene family. Our findings provide novel insights in the evolution of R gene clusters conferring late-blight resistance in Solanum spp.
Expression of the Medicago truncatula DMI2 Gene Suggests Roles of the Symbiotic Nodulation Receptor Kinase in Nodules and During Early Nodule Development
Authors: Bersoult Anne , Camut Sylvie , Perhald Ariana , Kereszt Attila , Kiss György B. , Cullimore Julie V.
Published: May 2007

The Medicago truncatula DMI2 gene encodes a receptorlike kinase required for establishing root endosymbioses. The DMI2 gene was shown to be expressed much more highly in roots and nodules than in leaves and stems. In roots, its expression was not altered by nitrogen starvation or treatment with lipochitooligosaccharidic Nod factors. Moreover, the DMI2 mRNA abundance in roots of the nfp, dmi1, dmi3, nsp1, nsp2, and hcl symbiotic mutants was similar to the wild type, whereas lower levels in some dmi2 mutants could be explained by regulation by the nonsense-mediated decay, RNA surveillance mechanism. Using pDMI2::GUS fusions, the expression of DMI2 in roots appeared to be localized primarily in the cortical and epidermal cells of the younger, lateral roots and was not observed in the root apices. Following inoculation with Sinorhizobium meliloti, the DMI2 gene was induced in the nodule primordia, before penetration by the infection threads. No increased expression was seen in lateral-root primordia. In nodules, expression was observed primarily in a few cell layers of the preinfection zone. These results are consistent with the DMI2 gene mediating Nod factor perception and transduction leading to rhizobial infection, not only in root epidermal cells but also during nodule development.