bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive phenotypic plasticity and plant water use
Authors: Nicotra Adrienne B. , Davidson Amy
Published: February 2010

The emergence of new techniques in plant science, including molecular and phenomic tools, presents a novel opportunity to re-evaluate the way we examine the phenotype. Our increasing capacity for phenotyping means that not only can we consider increasing numbers of species or varieties, but also that we can effectively quantify the phenotypes of these different genotypes under a range of environmental conditions. The phenotypic plasticity of a given genotype, or the range of phenotypes, that can be expressed dependent upon environment becomes something we can feasibly assess. Of particular importance is phenotypic variation that increases fitness or survival – adaptive phenotypic plasticity. Here, we examine the case of adaptive phenotypic plasticity in plant water use traits and consider how taking an ecological and evolutionary perspective on plasticity in these traits might have relevance for agriculture, horticulture and the management of native and invasive plant species in an era of rapid climate change.
Induction of ectopic Myc target gene JAG2 augments hypoxic growth and tumorigenesis in a human B-cell model
Authors: Yustein Jason T. , Liu Yen-Chun , Gao Ping , Jie Chunfa , Le Anne , Vuica-Ross Milena , Chng Wee Joo , Eberhart Charles G. , Bergsagel P. Leif , Dang Chi V.
Published: February 2010

Ectopic Myc expression plays a key role in human tumorigenesis, and Myc dose-dependent tumorigenesis has been well established in transgenic mice, but the Myc target genes that are dependent on Myc levels have not been well characterized. In this regard, we used the human P493-6 B cells, which have a preneoplastic state dependent on the Epstein–Barr viral EBNA2 protein and a neoplastic state with ectopic inducible Myc, to identify putative ectopic Myc target genes. Among the ectopic targets, JAG2 that encodes a Notch receptor ligand Jagged2, was directly induced by Myc. Inhibition of Notch signaling through RNAi targeting JAG2 or the γ-secretase Notch inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-(S)-phenylglycine t-butyl ester (DAPT) preferentially inhibited the neoplastic state in vitro. Furthermore, P493-6 tumorigenesis was inhibited by DAPT in vivo. Ectopic expression of JAG2 did not enhance aerobic cell proliferation, but increased proliferation of hypoxic cells in vitro and significantly increased in vivo tumorigenesis. Furthermore, the expression of Jagged2 in P493-6 tumors often overlapped with regions of hypoxia. These observations suggest that Notch signaling downstream of Myc enables cells to adapt in the tumor hypoxic microenvironment.
NANOS2 interacts with the CCR4-NOT deadenylation complex and leads to suppression of specific RNAs
Authors: Suzuki Atsushi , Igarashi Katsuhide , Aisaki Ken-ichi , Kanno Jun , Saga Yumiko
Published: February 2010

Nanos is one of the evolutionarily conserved proteins implicated in germ cell development. We have previously shown that NANOS2 plays an important role in both the maintenance and sexual development of germ cells. However, the molecular mechanisms underlying these events have remained elusive. In our present study, we found that NANOS2 localizes to the P-bodies, known centers of RNA degradation that are abundantly accumulated in male gonocytes. We further identified by immunoprecipitation that the components of the CCR4-NOT deadenylation complex are NANOS2-interacting proteins and found that NANOS2 promotes the localization of CNOT proteins to P-bodies in vivo. We also elucidated that the NANOS2/CCR4-NOT complex has deadenylase activity in vitro, and that some of the RNAs implicated in meiosis interact with NANOS2 and are accumulated in its absence. Our current data thus indicate that the expression of these RNA molecules is normally suppressed via a NANOS2-mediated mechanism. We propose from our current findings that NANOS2-interacting RNAs may be recruited to P-bodies and degraded by the enzymes contained therein through NANOS2-mediated deadenylation.
Translation efficiency is determined by both codon bias and folding energy
Authors: Tuller Tamir , Waldman Yedael Y. , Kupiec Martin , Ruppin Eytan
Published: February 2010

Synonymous mutations do not alter the protein produced yet can have a significant effect on protein levels. The mechanisms by which this effect is achieved are controversial; although some previous studies have suggested that codon bias is the most important determinant of translation efficiency, a recent study suggested that mRNA folding at the beginning of genes is the dominant factor via its effect on translation initiation. Using the
Escherichia coli
and
Saccharomyces cerevisiae
transcriptomes, we conducted a genome-scale study aiming at dissecting the determinants of translation efficiency. There is a significant association between codon bias and translation efficiency across all endogenous genes in
E. coli
and
S. cerevisiae
but no association between folding energy and translation efficiency, demonstrating the role of codon bias as an important determinant of translation efficiency. However, folding energy does modulate the strength of association between codon bias and translation efficiency, which is maximized at very weak mRNA folding (i.e., high folding energy) levels. We find a strong correlation between the genomic profiles of ribosomal density and genomic profiles of folding energy across mRNA, suggesting that lower folding energies slow down the ribosomes and decrease translation efficiency. Accordingly, we find that selection forces act near uniformly to decrease the folding energy at the beginning of genes. In summary, these findings testify that in endogenous genes, folding energy affects translation efficiency in a global manner that is not related to the expression levels of individual genes, and thus cannot be detected by correlation with their expression levels.
Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency
Authors: Gonzalez Rodolfo , Jennings Lori L. , Knuth Mark , Orth Anthony P. , Klock Heath E. , Ou Weija , Feuerhelm Julie , Hull Mitchell V. , Koesema Eric , Wang Yuping , Zhang Jia , Wu Chunlei , Cho Charles Y. , Su Andrew I. , Batalov Serge , Chen Hong , Johnson Kristen , Laffitte Bryan , Nguyen Deborah G. , Snyder Evan Y. , Schultz Peter G. , Harris Jennifer L. , Lesley Scott A.
Published: February 2010

Approximately 3,500 mammalian genes are predicted to be secreted or single-pass transmembrane proteins. The function of the majority of these genes is still unknown, and a number of the encoded proteins might find use as new therapeutic agents themselves or as targets for small molecule or antibody drug development. To analyze the physiological activities of the extracellular proteome, we developed a large-scale, high-throughput protein expression, purification, and screening platform. For this study, the complete human extracellular proteome was analyzed and prioritized based on genome-wide disease association studies to select 529 initial target genes. These genes were cloned into three expression vectors as native sequences and as N-terminal and C-terminal Fc fusions to create an initial collection of 806 purified secreted proteins. To determine its utility, this library was screened in an OCT4-based cellular assay to identify regulators of human embryonic stem-cell self-renewal. We found that the pigment epithelium-derived factor can promote long-term pluripotent growth of human embryonic stem cells without bFGF or TGFβ/Activin/Nodal ligand supplementation. Our results further indicate that activation of the pigment epithelium-derived factor receptor-Erk1/2 signaling pathway by the pigment epithelium-derived factor is sufficient to maintain the self-renewal of pluripotent human embryonic stem cells. These experiments illustrate the potential for discovering novel biological functions by directly screening protein diversity in cell-based phenotypic or reporter assays.
Aberrant overexpression and function of the miR-17-92 cluster in
MLL
-rearranged acute leukemia
Authors: Mi Shuangli , Li Zejuan , Chen Ping , He Chunjiang , Cao Donglin , Elkahloun Abdel , Lu Jun , Pelloso Luis A. , Wunderlich Mark , Huang Hao , Luo Roger T. , Sun Miao , He Miao , Neilly Mary Beth , Zeleznik-Le Nancy J. , Thirman Michael J. , Mulloy James C. , Liu Paul P. , Rowley Janet D. , Chen Jianjun
Published: February 2010

MicroRNA (miRNA)-
17-92
cluster (miR-17-92), containing seven individual miRNAs, is frequently amplified and overexpressed in lymphomas and various solid tumors. We have found that it is also frequently amplified and the miRNAs are aberrantly overexpressed in mixed lineage leukemia (
MLL
)-rearranged acute leukemias. Furthermore, we show that MLL fusions exhibit a much stronger direct binding to the locus of this miRNA cluster than does wild-type MLL; these changes are associated with elevated levels of histone H3 acetylation and H3K4 trimethylation and an up-regulation of these miRNAs. We further observe that forced expression of this miRNA cluster increases proliferation and inhibits apoptosis of human cells. More importantly, we show that this miRNA cluster can significantly increase colony-forming capacity of normal mouse bone marrow progenitor cells alone and, particularly, in cooperation with MLL fusions. Finally, through combinatorial analysis of miRNA and mRNA arrays of mouse bone marrow progenitor cells transfected with this miRNA cluster and/or MLL fusion gene, we identified 363 potential miR-17-92 target genes that exhibited a significant inverse correlation of expression with the miRNAs. Remarkably, these potential target genes are significantly enriched (
P
< 0.01; >2-fold) in cell differentiation, hematopoiesis, cell cycle, and apoptosis. Taken together, our studies suggest that overexpression of miR-17-92 cluster in
MLL
-rearranged leukemias is likely attributed to both DNA copy number amplification and direct up-regulation by MLL fusions, and that the miRNAs in this cluster may play an essential role in the development of
MLL
-associated leukemias through inhibiting cell differentiation and apoptosis, while promoting cell proliferation, by regulating relevant target genes.
Comparative analysis of integrative self‐knowledge, mindfulness, and private self‐consciousness in predicting responses to stress in Iran
Authors: Ghorbani Nima , Cunningham Christopher J. L. , Watson P. J.
Published: February 2010

Previous research has established that awareness of self‐experience is a stress resistance resource. The present study conducted an analysis of measures that record different aspects of self‐awareness (private self‐consciousness, mindfulness, and integrative self‐knowledge) to explain this stress‐resistance effect in a sample of Iranian university students (N=186). These students responded to Mindfulness Attention Awareness, Private Self‐Consciousness, Integrative Self‐Knowledge, and Perceived Stress Scales just before the stress of a 20‐day final examination period, and they then responded to Symptom Checklist and Vitality measures at four‐day intervals during the final examinations. Prior to final examinations, the three self‐awareness variables correlated positively with each other and negatively with perceived stress. Regression analyses of the data obtained during final examinations identified mindfulness to be a better operationalization of this stress‐resistance resource than private self‐consciousness. Specifically, mindfulness but not private self‐consciousness was a positive predictor of vitality and a negative predictor of symptoms. Hierarchical regression analyses also demonstrated that mindfulness and integrative self‐knowledge both explained resistance to physical symptoms, while integrative self‐knowledge functioned as a protective factor toward one's vitality. These data confirm the positive impact that self‐awareness has during stress and highlight the importance of considering both mindfulness and integrative self‐knowledge in understanding stress‐resistance processes.
The use of visual context during the production of referring expressions
Authors: Fukumura Kumiko , van Gompel Roger P. G. , Pickering Martin J.
Published: February 2010

Most theories of reference assume that a referent's saliency in the linguistic context determines the choice of referring expression. However, it is less clear whether cognitive factors relating to the nonlinguistic context also have an effect. We investigated whether visual context influences the choice of a pronoun over a repeated noun phrase when speakers refer back to a referent in a preceding sentence. In Experiment 1, linguistic mention as well as visual presence of a competitor with the same gender as the referent resulted in fewer pronouns for the referent, suggesting that both linguistic and visual context determined the choice of referring expression. Experiment 2 showed that even when the competitor had a different gender from the referent, its visual presence reduced pronoun use, indicating that visual context plays a role even if the use of a pronoun is unambiguous. Thus, both linguistic and nonlinguistic information affect the choice of referring expression.
Analysis of time-resolved optical emission of He cryoplasma at atmospheric pressure
Authors: Choi Jai Hyuk , Noma Yuri , Sano Masaki , Terashima Kazuo
Published: February 2010

Cryogenic plasma, so-called cryoplasma, was generated under helium at atmospheric pressure at temperatures ranging between room temperature and 79 K. Time-resolved emission spectra of the main species of the He cryoplasmas were measured in order to analyse the optical characteristics that can define the discharge mode. The experimental results clearly show that a decrease in temperature changes the temporal variation of radiation of the measured species and induces a transition of the discharge mode, from pseudoglow to glow, and then to Townsend discharge. This result reconfirms the scenario of temperature-dependent mode transition of cryoplasma.
Properties of the state of the art of bulk III–V nitride substrates and homoepitaxial layers
Authors: Freitas Jaime A
Published: February 2010

The technological importance of III–V nitride semiconductors relies on their variety of applications, which cover optical, optoelectronic and electronic devices capable of operating under extreme values of current, voltage and temperature. The major roadblock for full realization of the potential of nitride semiconductors is still the availability of affordable large-area and high-quality native substrates with controlled electrical properties. Despite the impressive accomplishments recently achieved by techniques such as hydride vapour phase epitaxy and ammonothermal for GaN and sublimation for AlN, much more must be attained before establishing a bulk growth technique of choice to grow these materials. A brief review of the structural, optical and electronic properties of the state of the art of bulk and thick-film (quasi-bulk) nitride substrates and homoepitaxial films is presented, and a few device applications are also highlighted.
High performance nonvolatile memory using SiO2/SiOx/SiOxNy stack on excimer laser-annealed polysilicon and the effect of blocking thickness on operation voltage
Authors: Van Duy Nguyen , Jung Sungwook , Kim Kwangryul , Son Dang Ngoc , Nga Nguyen Thanh , Cho Jaehyun , Choi Byoungdeog , Yi Junsin
Published: February 2010

Silicon-rich SiO
x
material is a good charge storage candidate for memory applications that promise a large memory window and low operation voltage. Nonvolatile memory (NVM) devices fabricated on excimer laser-annealed polysilicon using SiO2/SiO
x
/SiO
x
N
y
(OOxOn) structure are investigated with SiO2 blocking thicknesses changing from 15 to 20 to 30 nm. The Si-rich SiO
x
material exposed numerous non-bridging oxygen hole-centre defect sources and a rich silicon phase in the base material. These defects, as well as amorphous silicon clusters existing in the SiO
x
layer, enhance the charge storage capacity of the device. Retention properties were ensured by 3.2 nm SiO
x
N
y
tunnelling layer growth via N2O plasma-assisted oxynitridation. NVM characteristics showed a retention exceeding 85% of the threshold voltage shift after 104 s and greater than 70% after 10 years. Depending on the blocking thickness of 15, 20 or 30 nm, operating voltages varied from ±9 to ±13 V at a programming/erasing duration of only 1 ms. These excellent operating properties of the OOxOn structure make it a potential competitor among the new generation of memory structures on glass.
Three distinct modes in a cold atmospheric pressure plasma jet
Authors: Walsh J L , Iza F , Janson N B , Law V J , Kong M G
Published: February 2010

Cold atmospheric pressure helium plasma jets are increasingly used in many processing applications, due to a distinct combination of their inherent plasma stability with excellent reaction chemistry often enhanced downstream. Despite their widespread usage, it remains largely unknown whether cold atmospheric plasma jets maintain similar characteristics from breakdown to arcing or whether they possess different operating modes. In addition to their known ability to produce a fast moving train of discrete luminous clusters along the jet length, commonly known as plasma bullets, this paper reports evidence of two additional modes of operation, namely a chaotic mode and a continuous mode in an atmospheric helium plasma jet. Through detailed electrical and optical characterization, it is shown that immediately following breakdown the plasma jet operates in a deterministic chaotic mode. With increasing input power, the discharge becomes periodic and the jet plasma is found to produce at least one strong plasma bullet every cycle of the applied voltage. Further increase in input power eventually leads to the continuous mode in which excited species are seen to remain within the inter-electrode space throughout the entire cycle of the applied voltage. Transition from the chaotic, through the bullet, to the continuous modes is abrupt and distinct, with each mode having a unique set of operating characteristics. For the bullet mode, direct evidence is presented to demonstrate that the evolution of the plasma jet involves a repeated sequence of generation, collapse and regeneration of the plasma head occurring at locations progressively towards the instantaneous cathode. These offer previously unavailable insight into plasma jet formation mechanisms and the potential of matching plasma jet modes to specific needs of a given processing application.
Thickness and annealing effects on the optoelectronic properties of ZnS films
Authors: Mohamed S H , El-Hagary M , Emam-Ismail M
Published: February 2010

ZnS films were prepared with different thicknesses by electron beam evaporation on glass substrates. The films were annealed in air atmosphere at different annealing temperatures and times. The x-ray diffraction patterns indicate that the increase in film thickness resulted in good crystallinity of the ZnS film. The ZnS film transforms to mixed ZnS and ZnO upon annealing at 500 °C. The optical band gap (E
g) values decrease from 3.70 to 3.43 eV as the thickness increases from 50 to 400 nm. The transmittance is affected strongly by annealing. Annealing at 400 °C enhances the visible range transmittance and the quality of the film. The E
g values are not affected by the annealing time at 400 °C, while the refractive index decreases with increasing annealing time. The figure of merit revealed that the ZnS film annealed at 400 °C and coated with 8 nm zinc top layer is the best candidate for use as transparent conductive electrodes.
Tunneling and transmission resonances of a Dirac particle by a double barrier
Authors: Villalba Víctor M , González-Árraga Luis A
Published: February 2010

We calculate the tunneling process of a Dirac particle across two square barriers separated by a distance d, as well as the scattering by a double-cusp barrier, where the centers of the cusps are separated by a distance larger than their screening lengths. Using the scattering matrix formalism, we obtain the transmission and reflection amplitudes for the scattering processes of both configurations. We show that the presence of transmission resonances modifies the Lorentzian shape of the energy resonances and induces the appearance of additional maxima in the transmission coefficient in the range of energies where transmission resonances occur. We calculate the Wigner time delay and show how their maxima depend on the position of the transmission resonance.
Two kinds of multi-order exact solution to the shallow water system
Authors: Fu Zuntao , Zhang Linna , Mao Jiangyu , Liu Shikuo
Published: February 2010

In this paper, two kinds of Lamé function have been listed and compared. Based on these two Lamé functions and the Jacobi elliptic function, the perturbation method is applied to the shallow water system, and many multi-order solutions of novel form are derived. In addition, it is shown that different Lamé functions can exist in the first-order solutions of the nonlinear system.
Scaling laws for large magneto-optical traps
Authors: Gattobigio G L , Pohl T , Labeyrie G , Kaiser R
Published: February 2010

Multiple scattering of light has been the main limitation of the maximum atomic density achievable in magneto-optical traps (MOTs). We present a detailed experimental investigation of the size and density scaling laws for large MOTs with up to N=1010 atoms, larger than those usually studied in detail. Most of our observations can be explained with previous models and only a few regimes show unexplained deviations. We also propose a new repulsion mechanism, based on the rescattered repumper photons that might limit the atomic density of atoms when the optical thickness for repumper light becomes important, adding an additional ingredient in the complexity of large MOTs.
Age and growth estimates for the starry smoothhound (Mustelus asterias) in the Northeast Atlantic Ocean
Authors: Farrell Edward D. , Mariani Stefano , Clarke Maurice W.
Published: February 2010

Farrell, E. D., Mariani, S., and Clarke, M. W. 2010. Age and growth estimates for the starry smoothhound (Mustelus asterias) in the Northeast Atlantic Ocean. – ICES Journal of Marine Science, 67: 931–939. Age, growth, and longevity were estimated for the starry smoothhound (Mustelus asterias), based on the interpretation of sectioned vertebrae of 106 males (35–104 cm stretch total length, STL) and 114 females (44–112 cm STL). Growth curves were fitted to length-at-age data using von Bertalanffy and Gompertz models. The three-parameter von Bertalanffy growth function (VBGF) provided the best statistical fit to the male data (L∞ = 103.7 cm STL, L0 = 38.1 cm STL, k = 0.195 year−1). The Gompertz growth function provided the best statistical fit to the female data, although the estimated parameters were biologically unreasonable. Therefore, the three-parameter VBGF was also accepted for females (L∞ = 123.5 cm STL, L0 = 34.9 cm STL, k = 0.146 year−1). Longevity was estimated to be 13 and 18.3 years for males and females, respectively. The length–weight relationship is also presented for 304 male and 424 female M. asterias. The von Bertalanffy model was fitted to the weight-at-age data. These estimates can form the basis of future work on the assessment and management of this species.
Between-year variability in the mixing of North Sea herring spawning components leads to pronounced variation in the composition of the catch
Authors: Bierman Stijn M. , Dickey-Collas Mark , van Damme Cindy J. G. , van Overzee Harriët M. J. , Pennock-Vos M. G. , Tribuhl Silja V. , Clausen Lotte A. W.
Published: February 2010

Bierman, S. M., Dickey-Collas, M., van Damme, C. J. G., van Overzee, H. M. J., Pennock-Vos, M. G., Tribuhl, S. V., and Clausen, L. A. W. 2010. Between-year variability in the mixing of North Sea herring spawning components leads to pronounced variation in the composition of the catch. – ICES Journal of Marine Science, 67: 885–896. North Sea herring (Clupea harengus) are managed as a single stock, but maintaining a diversity of spawning components is considered important. However, the total catch from each of these components cannot be estimated easily because the components mix during the summer feeding season. The spawning origin of herring is determined from patterns in the microstructure of the otolith core, from samples taken in the central and northern North Sea during summer of 2004–2007. The annual catch composition of Dutch vessels is determined within a statistical framework that takes account of the spatial patterns in mixing of spawning components and the classification success of the method. Mixing of components varied between years, with steep latitudinal gradients in compositions in some years, resulting in pronounced between-year differences in estimated catch compositions. Differences in lengths-at-age between spawning components, in particular of the 2000 year class, may have caused the observed between-year changes in mixing of components. Our results indicate that estimates of compositions change when assumptions of perfect spatial mixing and perfect classification are relaxed, and can be uncertain in particular as a result of misclassifications, and that it may not be appropriate to assume that ratios between components are constant through time.
Uromyces ciceris-arietini, the Cause of Chickpea Rust: New Hosts in the Trifolieae, Fabaceae
Authors: Stuteville D. L. , Graves W. L. , Dixon L. J. , Castlebury L. A. , Minnis A. M.
Published: February 2010

Uromyces ciceris-arietini has been reported on Cicer arietinum (chickpea) and Medicago polyceratia. Plants of Medicago polymorpha in Riverside and San Diego, CA were collected with severe rust caused by U. ciceris-arietini. To confirm the identification and potential new host range, a monouredinial isolate of U. ciceris-arietini from M. polymorpha was inoculated on eight accessions each of C. arietinum and M. polyceratia. All plants showed symptoms of the disease. Consequently, a range of fabaceous hosts were evaluated for their reaction to U. ciceris-arietini. New hosts for U. ciceris-arietini included 29 species of Medicago, specifically M. arabica, M. blancheana, M. ciliaris, M. constricta, M. coronata, M. doliata, M. granadensis, M. intertexta, M. italica, M. laciniata, M. lanigera, M. lesinsii, M. lupulina, M. minima, M. murex, M. muricoleptis, M. orbicularis, M. praecox, M. radiata, M. rigidula, M. rotata, M. rugosa, M. sativa, M. sauvagei, M. scutellata, M. soleirolii, M. tenoreana, M. truncatula, and M. varia, and three species of Melilotus, specifically M. italicus, M. speciosus, and M. spicatus. This isolate of U. ciceris-arietini produced no symptoms on plants in the 33 accessions tested in the genera Anthyllis, Astragalus, Lotus, and Lupinus. DNA sequences are provided to aid in the identification of this pathogen.
Differential Reactions on Mature Green and Ripe Chili Fruit Infected by Three Colletotrichum spp.
Authors: Mongkolporn Orarat , Montri Paweena , Supakaew Thunyawan , Taylor Paul W. J.
Published: February 2010

Differential reactions on mature green and ripe chili fruit of 10 genotypes from four cultivated Capsicum spp. (i.e., Capsicum annuum, C. baccatum, C. chinense, and C. frutescens) were investigated after being inoculated with 33 isolates of Colletotrichum capsici, C. gloeosporioides, and C. acutatum originating from Thailand. The inoculation was performed using an injection method. Differential reactions, based on qualitative host reactions (i.e., lesion development versus no infection) grouped the Colletotrichum isolates into different pathotypes. C. capsici was grouped into three pathotypes based on differential reactions on ripe fruit stage of two Capsicum chinense genotypes (PBC932 and C04714) and two pathotypes based on differential reactions on mature green fruit stage of C04714. Colletotrichum gloeosporioides was grouped into five and six pathotypes on their reactions in ripe and green fruit maturity stages, respectively. C04714 and two Capsicum annuum genotypes (Jinda and Bangchang) acted as differential hosts with ripe fruit, whereas C04714 with all C. annuum and C. frutescens genotypes acted as differential hosts with green fruit. No pathotype of Colletotrichum acutatum was identified on ripe fruit but three pathotypes were identified on green fruit based on differential reactions in two Capsicum baccatum genotypes (PBC80 and PBC81).
Soil Treatments for the Potential Elimination of Phytophthora ramorum in Ornamental Nursery Beds
Authors: Yakabe L. E. , MacDonald J. D.
Published: February 2010

Ramorum leaf blight, caused by Phytophthora ramorum, has reemerged at several California nurseries after removal of infested material. In many cases, reemergence was not associated with reintroduction of the pathogen and may be attributed to inoculum surviving in soil beds because P. ramorum propagules can survive for over a year in soil. Using artificially infested soil in microcosms, fumigation and heat treatments were examined as potential eradicants of P. ramorum from soil. Treatments with chloropicrin, Vapam, and iodomethane were effective in reducing P. ramorum propagules below detection limits. Basamid was consistently effective only when fully incorporated into the soil. Application of Basamid (392 kg/ha) at infested ornamental nursery sites mirrored results from microcosm experiments, indicating that a tarp cover over treated soil is necessary for reliable efficacy. Dimethyldisulfide, 1,3-dichloropropene, and two formulations of hydrogen dioxide were less effective, resulting in only partial reduction of propagules. In heat treatments, P. ramorum in soil microcosms remained detectable 42 days after microcosms were incubated at 30 and 22°C but was not detectable in soil heated above 40°C for 3 days. Results from a solarized field plot indicate that prolonged sublethal temperatures, between 35 and 40°C for 42 days, can be effective in eliminating detectable propagules of P. ramorum.
Effectiveness of Chemo- and Thermotherapeutic Treatments on Pepino mosaic virus in Tomato Seed
Authors: Ling Kai-Shu
Published: February 2010

Pepino mosaic virus (PepMV) is a seedborne virus of importance in greenhouse tomato. The ease of mechanical transmission of PepMV from contaminated tomato seed to seedlings makes commercial tomato seed a potential source of initial virus inoculum. The objective of this study was to evaluate the effectiveness of chemo- and thermotherapeutic treatments on PepMV using seed from a commercial hybrid tomato seed lot. The effect of various seed treatments was evaluated through bioassay with mechanical inoculation of the treated seed extract on indicator plants (Nicotiana benthamiana). Three commonly used seed-treatment chemicals and two thermo-treatment methods were evaluated. The most effective chemical was the commercial bleach solution (0.5 and 1.0% sodium hypochlorite), followed by trisodium phosphate. On the other hand, hydrochloric acid treatments were not effective. Under the stated chemotherapeutic treatment conditions, the rate of seed germination was not significantly affected. With thermotherapeutic treatments, although hot water soaking for 2 h at 55°C deactivated virus infectivity, it also resulted in a detrimental effect on seed germination. However, treatment with dry-heat baking (72 or 80°C for 48 to 72 h) was effective in reducing PepMV infection with minimum impact on seed germination.
Changes in Fungicide Resistance Frequency and Population Structure of Pyricularia oryzae after Discontinuance of MBI-D Fungicides
Authors: Suzuki F. , Yamaguchi J. , Koba A. , Nakajima T. , Arai M.
Published: February 2010

The changes in fungicide resistance frequency and population structure of the rice blast fungus Pyricularia oryzae were monitored after the discontinuance of melanin biosynthesis inhibitor targeting scytalone dehydratase (MBI-D) fungicides use in Saga Prefecture, Japan. After discontinuance in 2003, the frequency of resistant isolates decreased from 71.8% in 2002 to 25% in 2003, and became undetectable in 2007. The initial marked decrease was due to a decline of isolates possessing the predominant haplotype, although the haplotypic diversity among resistant isolates remained high from 2003 to 2005. These results revealed that resistant isolates were less fit in comparison with sensitive isolates in the absence of MBI-D fungicide pressure under field conditions. Pairwise FST values indicated that the change in population structure after MBI-D discontinuance was explainable by a rapid change in the proportions of resistant and sensitive subpopulations. Depending upon the existence of fitness cost and rapid changes in population structure, it may be possible to reintroduce MBI-D fungicides in areas where resistance has already developed, although we speculate that fitness cost related to MBI-D resistance may be small based on our present results and previous findings.
Bacterial Canker of Sweet Cherry in Oregon—Infection of Horticultural and Natural Wounds, and Resistance of Cultivar and Rootstock Combinations
Authors: Spotts Robert A. , Wallis Kelly M. , Serdani Maryna , Azarenko Anita N.
Published: February 2010

This study was done to (i) compare seven types of natural or horticultural injuries and wounds for incidence, severity, and mortality of infection of sweet cherry (Prunus avium) by Pseudomonas syringae pv. syringae; (ii) determine the relative resistance to bacterial canker of 14 cultivar–rootstock combinations; (iii) determine if P. syringae pv. syringae is transmitted by contaminated pruning tools; and (iv) determine if summer and winter pruning cuts become resistant to infection. Infection occurred at all of the seven types of injury and wound sites on both cvs. Sunset Bing and Golden Heart. Infection of inoculated wounds made in spring and summer (heading cuts when trees were planted, scoring cuts, and summer pruning) resulted in the greatest canker incidence and severity. Inoculation of heading cuts resulted in the highest tree mortality (86%). ‘Bing’ and ‘Sweetheart’ were the most susceptible cultivars while ‘Regina’ and ‘Rainier’ appeared to be more resistant. Bing trees had the highest mortality of any cultivar with 70% dead at the end of the 3-year study. Canker severity of the three rootstocks varied considerably but mortality was greatest for trees on Gisela 6 (77%). Bacterial canker was not transmitted in summer or winter by cutting through active cankers, then immediately using the same pruning tool to make heading cuts on healthy trees. Heading cuts became resistant to infection after about 1 week in summer and 3 weeks in winter. Results are discussed as part of an integrated management program for bacterial canker of sweet cherry.
Cross Inoculation Tests with Phellinus noxius Isolates from Nine Different Host Plants in the Ryukyu Islands, Southwestern Japan
Authors: Sahashi Norio , Akiba Mitsuteru , Ishihara Makoto , Miyazaki Kazuhiro , Kanzaki Natsumi
Published: February 2010

Brown root rot, caused by Phellinus noxius, leads to problems in management of shade, ornamental, and windbreak trees in subtropical regions of the world, and it has been causing serious problems in Japan since 1988. To identify the pathogenicity, host specialization, and virulence of the pathogen, cross inoculation tests were carried out using isolates of the fungus obtained from nine different tree species. P. noxius was pathogenic to all of the nine tree species tested, and it killed inoculated seedlings. Among the 810 trees inoculated with the fungus, a total of 141 trees (17.4%), including all nine species, were dead within 110 days after inoculation. The first symptom of infection was rapid wilt with discoloration of leaves 20 to 30 days after inoculation, and then the plants quickly declined. Only one isolate of P. noxius that was tested caused significantly higher mortality in its original host than in other species, suggesting that the pathogen has little to no host specificity. However, the fungus did show variation in virulence, with the isolates originating in Bischofia javanica and Casuarina equisetifolia causing significantly higher mortality than those collected from other host species. More isolates of P. noxius from the same host species and/or from various countries should be studied to understand host specialization and virulence of the pathogen.
White Mold Management in Common Bean by Increasing Within-Row Distance Between Plants
Authors: Vieira R. F. , Paula Júnior T. J. , Teixeira H. , de S. Carneiro J. E.
Published: February 2010

White mold of common bean (Phaseolus vulgaris), caused by Sclerotinia sclerotiorum, is a major yield-limiting disease during the fall-winter season in Brazil. This study was conducted to evaluate the efficacy of decreasing within-row densities for an indeterminate growth habit (type IIIa) cultivar, keeping constant the between-row spacing of 0.5 m, to manage the disease. A modification of within-row plant distributions was also attempted in order to reduce white mold intensity. The study was conducted with sprinkler irrigation in two growing seasons (2000 and 2001) in Viçosa, State of Minas Gerais, Brazil, in an area naturally infested with sclerotia. In 2000, treatments were arranged as 3 × 2 × 2 factorial combination of within-row densities (15, 7.5, or 5 plants/m), within-row plant distributions (single and equidistant plants or equidistant groups of three plants), and fluazinam treatments (with or without). In 2001, 16, 12, 8, or 4 plants/m were combined with fluazinam treatments. Fluazinam was applied at both flowering onset and 10 or 13 days later. Average incidence was 92.6% in 2000 and 77.8% in 2001; severity index was 69.8% in 2000 and 40.2% in 2001; and yield was 1,656 kg/ha in 2000 and 2,542 kg/ha in 2001. White mold decreased and yield increased as within-row densities were reduced, regardless of fluazinam treatments. A distribution of equidistant groups of three plants was ineffective in reducing disease. The use of 4 equidistant plants/m in infested irrigated areas was an effective strategy in white mold management.
First Report of Alternaria Brown Spot of Citrus Caused by Alternaria alternata in Yunnan Province, China
Authors: Wang X. F. , Li Z. A. , Tang K. Z. , Zhou C. Y. , Yi L.
Published: February 2010

Brown spot of citrus is considered a major problem on the fruit of many citrus cultivars grown for fresh markets including tangerines (Citrus reticulata) and their hybrids. It causes lesions on leaves, stems, and fruit and reduces yield and fruit quality (2). In 2003 in southern Wenshan Municipality, Yunnan Province in China, sporadic occurrence of Alternaria brown spot was observed on Tangfang mandarin, a local citrus cultivar identified preliminarily as a kind of mandarin hybrid. From 2006 to 2008, nearly 80% of local orchards were infected with the disease. Fruit symptoms typical of Alternaria brown spot ranging from light brown, slightly depressed spots to circular and dark brown areas were observed. Leaves showed small, brown, circular spots and irregular blighted areas with characteristic yellow halos. Tissues from the margin of fruit spots or infected leaf parts of eight different trees were surface sterilized in 1.5% sodium hypochlorite for 1 min, plated on potato dextrose agar (PDA), and then incubated at 27°C in the dark for 1 week. Dark brown mycelia and pigmented septate conidia with lengths of 10 to 35 μm and widths of 5 to 13 μm were produced. On the basis of conidial morphological characteristics, the pathogen was identified as Alternaria alternata (Fr.:Fr.) Keissl (1). Detached young healthy leaves of ‘Minneola’ tangelo (C. reticulata × C. paradisi) were sprayed with a conidial suspension of 105 conidia per ml and incubated in a moist chamber at 27°C. A control treatment with an equal number of leaves was sprayed with distilled water only. After 48 h, seven of these isolates caused necrotic lesions on detached leaves, characteristic of the disease, whereas there were no symptoms on leaves of the water control. Pure cultures were recovered on PDA from symptomatic tissues and the morphological characteristics of the conidia closely fit the description of A. alternata, confirming Koch's postulates. Currently, the distribution of Alternaria brown spot of citrus is confined to southern Wenshan Municipality in Yunnan Province where it is a serious disease problem on the most important commercial cultivar in this region. The identification of the pathogen now allows for appropriate field management and control measures. To our knowledge, this is the first report of Alternaria brown spot of citrus in China.

References: (1) Z. Solel. Plant Pathol. 40:145, 1991. (2) J. O. Whiteside. Plant Dis. Rep. 60:326, 1976.
First Report of the Stubby Root Nematode, Paratrichodorus minor, in Mainland China
Authors: Li X. , Guo K. , Zhang Y. , Yan X. , Zheng J.
Published: February 2010

The stubby root nematode, Paratrichodorus minor (Colbran, 1956) Siddiqi, 1974, is an economically important species. It not only causes direct damage to the meristemic tissues of plants, but also can be a vector of Tobacco rattle virus and Pepper ringspot virus (2). It has been documented in Afghanistan, Argentina, Australia, Brazil, Canary Islands, Cuba, Egypt, Fiji, India, Israel, Ivory Coast, Japan, Java, Mauritania, New Zealand, Nicaragua, Philippines, Puerto Rico, Senegal, South Africa, Taiwan, Upper Volta, the United States, the former USSR, and Venezuela (1). During a recent investigation on Trichodoridae occurring in China, eight stubby root nematode populations were detected in Hainan, Yunnan, and Fujian provinces in the rhizospheres of eggplant (Solanum melongena), Chinaberry (Melia azedarach), lettuce (Lactuca sativa), longan (Dimocarpus longan), peach (Prunus persica), pear (Pyrus sp.), and walnut (Juglans regia) in soils ranging from clay to sand. The eight populations had similar morphological and molecular characters. The females were cigar shaped with rod-shaped vaginal sclerotization parallel to the longitudinal body axis with a quadrangular vagina in side view having a short vulval slit. The key morphometrics of females were consistent with those of P. minor: body length, 631 to 757 μm; body diameter, 27 to 43 μm; onchiostyle, 35 to 36 μm; a, 18 to 24; b, 4.9 to 5.5; v%, 53 to 55; length of vagina, 10.8 to 11.1 μm; and size of vaginal pieces, 1.7 to 1.9 μm. Males in P. minor are rare and were not found in any of the eight populations. Partial sequences of the 18s RNA gene of each population were amplified with forward primer 5′-AAA GAT TAA GCC ATG CAT G-3′ (2), and reverse primer 5′-AGT CAA ATT AAG CCG CAG-3′ (3), which yielded a PCR fragment of 1,153 bp. PCR products from all eight populations were sequenced and submitted to GenBank and assigned Accession Nos. GQ995703, GQ995704, GQ995705, GQ995706, GQ995707, GQ995708, GQ995709, and GQ995710. The sequences exhibited 99.8 to 100% similarity with those of P. minor isolates DQ345526, AM269897, AJ438052, AJ438053, and AJ438058 from GenBank. Morphological and molecular identification confirmed that all populations were P. minor. To our knowledge, this is the first report of P. minor in mainland China.

References: (1) K. Boutsika et al. Nematology 6:145, 2004. (2) W. Decramer. The Family Trichodiridae: Stubby Root and Virus Vector Nematodes. Kluwer Academic Publishers, Dordrecht, the Netherlands, 1995. (3) I. S. Waite et al. Soil Biol. Biochem. 35:1165, 2003.
Occurrence of Potato Soft Rot Caused by Erwinia carotovora (synonym Pectobacterium carotovorum) in Nepal: A First Report
Authors: Lamichhane J. R. , Balestra G. M. , Varvaro L.
Published: February 2010

Potato (Solanum tuberosum L.) is the fourth most important major crop of Nepal after rice, corn, and wheat, with an annual production of 1.94 million t and 153,000 ha of harvested area. It is a staple food crop in the remote hilly areas and the main vegetable in other parts of the country. Potato is grown in all three major agricultural zones (high hills, mid hills, and plain land) of Nepal, at an altitude ranging from 60 m to more than 4,000 m. Erwinia carotovora causes soft rot worldwide on a wide range of hosts including potato, carrot, and cabbage. During the spring of 2009, a soft rot with a foul smell was noted in stored potato tubers of different local cultivars, especially Rato Alu and Seto Alu, in the Kathmandu District, central region of Nepal. Symptoms on tubers appeared as tan, water-soaked areas with watery ooze. The rotted tissues were white-to-cream colored. Seven different potato fields, where the stored tubers originated, were surveyed and 23 samples consisting of approximately three symptomatic tubers were collected. Bacteria were successfully isolated from all diseased tissues on nutrient agar supplemented with 5% sucrose and incubated at 26 ± 1°C. After purification on tripticase soy agar medium, 17 isolates were identified as E. carotovora by the following deterministic tests: all strains were gram-negative rods; oxidase negative; facultatively anaerobic; able to degrade pectate; sensitive to erythromycin; negative for phosphatase; unable to produce acid from α-methyl-glucoside; and produced acid from trehalose. Pathogenicity of the strains was evaluated by depositing a bacterial suspension (106 CFU/ml) on potato slices (cv. Monalisa) and incubating at 30 ± 1°C. A reference strain of E. carotovora subsp. carotovora (NCPPB 2577) and sterile distilled water were used, respectively, as positive and negative controls. All strains caused soft rot within a week. Bacteria were reisolated from the slices and were shown to be identical to the original strains according to the above morphological, cultural, and biochemical tests. A 1,430-bp region of the 16S rDNA from all strains was amplified with primers NOC 1F (AGAGTTTGATCATGGCTCAG) and NOC 3R (ACGGTTACCTTGTTACGACTT) and sequenced (GenBank Accession No. GU075708; strain NEP ECC09). A BlastN search of GenBank revealed that the strains had 100% nt identity with the 16S rDNA sequence of E. carotovora subsp. carotovora type strain ATCC 15713 (GenBank Accession No. U80197). The finding of this pathogen is of fundamental value since this crop represents one of the economically important crops of Nepal. This pathogen has already been reported in the countries of China and India (1) with whom Nepal shares its boundaries. The pathogen may have been introduced to this region of Nepal via seed potato tubers from other countries.

Reference: (1) G. S. Shekhawat et al. Potato Res. 19:241, 1976.
Distinguishing Heterodera filipjevi and H. avenae Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism and Cyst Morphology
Authors: Yan Guiping , Smiley Richard W.
Published: February 2010

The cereal cyst nematodes Heterodera filipjevi and H. avenae impede wheat production in the Pacific Northwest (PNW). Accurate identification of cyst nematode species and awareness of high population density in affected fields are essential for designing effective control measures. Morphological methods for differentiating these species are laborious. These species were differentiated using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer (ITS)-ribosomal (r)DNA with up to six restriction endonucleases (TaqI, HinfI, PstI, HaeIII, RsaI, and AluI). The method was validated by inspecting underbridge structures of cyst vulval cones. Grid soil sampling of an Oregon field infested by both species revealed that H. filipjevi was present at most of the infested grid sites but mixtures of H. avenae and H. filipjevi also occurred. These procedures also detected and differentiated H. filipjevi and H. avenae in soil samples from nearby fields in Oregon and H. avenae in samples from Idaho and Washington. Intraspecific polymorphism was not observed within H. filipjevi or PNW H. avenae populations based on the ITS-rDNA. However, intraspecific variation was observed between H. avenae populations occurring in the PNW and France. Methods described here will improve detection and identification efficiencies for cereal cyst nematodes in wheat fields.