bluuebunny/crossref_metadata_2025 huggingface dataset:
Transmittance and optical constants of Pr films in the 4–1600eV spectral range
Authors: Fernández-Perea Mónica , Vidal-Dasilva Manuela , Aznárez José A. , Larruquert Juan I. , Méndez José A. , Poletto Luca , Garoli Denis , Malvezzi A. Marco , Giglia Angelo , Nannarone Stefano
Published: June 2008

The optical constants of Pr films were obtained in the 4–1600eV range from transmittance measurements performed at room temperature. Thin films of polycrystalline Pr were deposited by evaporation in ultrahigh vacuum conditions and their transmittance was measured in situ. Pr films were deposited onto grids coated with a thin, C support film. Transmittance measurements were used to obtain the optical extinction coefficient k of Pr films in the 4–1600 investigated photon energy range. The refractive index n of Pr was calculated using the Kramers–Krönig analysis. Data were extrapolated both on the high and low-energy sides by using experimental and calculated extinction coefficient data available from the literature. Pr, similar to other lanthanides, has a low-absorption band right below the O2,3 edge onset; the lowest absorption was measured at about 17eV. Therefore, Pr is a promising material for filters and multilayer coatings in the energy range below O2,3 edge in which most materials have a strong absorption. A good consistency of the data were obtained through f and inertial sum rules.
Semiconducting nature of the oxygen-adsorbed graphene sheet
Authors: Ito Jun , Nakamura Jun , Natori Akiko
Published: June 2008

Structural and electronic properties for oxygen-adsorbed graphene sheets have been explored using first-principles total-energy calculations within the local density functional theory. A finite energy gap emerges for the oxygen-adsorbed graphene and its value increases with the ratio of O∕C, as manifested by experiments. Further, adsorption energy and migration barrier for oxygen atoms on the graphene sheet have been investigated. The results show that isolated oxygen atoms are highly mobile and incline to condense on the graphene sheet.
Compact electron beam ion trap for spectroscopy of moderate charge state ions
Authors: Nakamura Nobuyuki , Kikuchi Hiroyuki , Sakaue Hiroyuki A. , Watanabe Tetsuya
Published: June 2008

A compact electron beam ion trap (EBIT) has been constructed for spectroscopic studies of moderate charge state ions. The electron beam energy range of the present EBIT is 100–1000eV, for which it is rather difficult to operate an ordinary EBIT which used to be designed for operation with higher electron energy (∼10keV or more). To cut down the running costs, a superconducting wire with a high critical temperature is used for the central magnet so that it can be operated without liquid helium. The performance of the compact EBIT has been investigated through visible spectroscopy of highly charged krypton and iron ions.
Local probing of relaxation time distributions in ferroelectric polymer nanomesas: Time-resolved piezoresponse force spectroscopy and spectroscopic imaging
Authors: Rodriguez Brian J. , Jesse Stephen , Kim Jihee , Ducharme Stephen , Kalinin Sergei V.
Published: June 2008

Time-resolved piezoresponse force spectroscopy (TR-PFS) and spectroscopic imaging are developed to probe the spatial variability of relaxation behavior in nanoscale ferroelectric materials and structures. TR-PFS was applied to study polarization dynamics in polyvinylidine fluoride and trifluoroethylene nanomesas. We demonstrate that polarization relaxation in ferroelectric polymers is slow even on the ∼10nm length scale of piezoresponse force microscopy (PFM) signal generation. Furthermore, the relaxation times are found to be nonuniform within the nanomesa, indicative of a complex internal structure. The applicability of TR-PFM for studies of polarization dynamics in ferroelectric polymers and relaxors is discussed.
Demonstration of enhancement-mode GaAs metal-insulator-semiconductor field effect transistor with channel inversion using Si3N4 as gate dielectric
Authors: Zheng J. F. , Tsai W. , Li W. P. , Wang X. W. , Ma T. P.
Published: June 2008

We report n-channel enhancement-mode GaAs metal-insulator-semiconductor Field Effect Transistors (MISFETs) with ∼6nm equivalent oxide thickness of molecular-and-atomic (MAD) depositioned Si3N4 as the gate dielectric. The GaAs based MISFETs were fabricated using a gate-first process that preserved the channel inversion characteristic in MIS capacitor structures [W. P. Li, X. W. Wang, Y. X. Liu, and T. P. Ma, Appl. Phys. Lett. 90, 193503 (2007)]. The channel inversion characteristics of the GaAs MIS capacitors, measured by the quasistatic C-V (capacitor-voltage) technique, were well maintained throughout the entire fabrication process with temperatures up to 800°C. C-V hysteresis as small as 100mV was achieved. The Si3N4-gated GaAs MISFETs clearly demonstrated the enhancement-mode, gate-modulated Id-Vd transfer characteristics with channel inversion.
Highly efficient red organic light-emitting devices based on a fluorene-triphenylamine host doped with an Os(II) phosphor
Authors: Wu Chen-Hao , Shih Ping-I , Shu Ching-Fong , Chi Yun
Published: June 2008

We report highly efficient red-light-emitting devices based on a fluorene-triphenylamine tris[4-(9-phenylfluoren-9-yl)phenyl]amine (TFTPA) host doped with an osmium phosphor. The sterically hindered fluorene peripheries provided a compatible environment for the osmium dopant and alleviated concentration quenching of the phosphor at high doping levels. Increasing the doping concentration from 7to21wt% dramatically decreased the driving voltage of the TFTPA-based devices, leading to improved power efficiency. The 21wt% Os-doped device exhibited maximum luminous and powder efficiencies of 29.9cd∕A and 25.2lm∕W, combined with high efficiencies at high brightness. At 1000cd∕m2 the efficiencies remained 29.2cd∕A and 22.2lm∕W.
Thermal properties of calcium doped strontium barium niobate crystal
Authors: Gao Ch. Y. , Xia H. R. , Xu J. Q. , Zhou C. L. , Zhang H. J. , Wang J. Y.
Published: June 2008

Calcium doped strontium barium niobate is a tungsten-bronze ferroelectric crystal with a tetragonal unit cell. Thermophysical properties including specific heat, thermal expansion, and thermal diffusion were performed on a single crystal (Ca0.28Ba0.75)0.25(Sr0.60Ba0.40)0.75Nb2O6 (CSBN25) to determine thermal behaviors along the a and c axes. Negative thermal expansion was observed along the c axes below the Curie temperature. Isotropic thermal behavior (thermal diffusion and thermal conductivity) was observed around Curie temperature. The abnormal thermal behaviors are considered as arising due to the geometry of the dope-affected crystal.
Temporary transition in suspended carbon nanotubes
Authors: Syue Sen-Hong , Kuo Hsin-Fu , Hsu Ching-Tung , Chen Hung-Jen , Chen Uei-Shin , Hsu Wen-Kuang , Shih Han-Chang
Published: June 2008

A semiconducting phase is temporarily present in doped carbon nanotube after field treatment and underlying mechanism involves chemical potential change and EF movement by field induced charge accumulation. Metallic phase re-emerges as accumulated charges are released.
Interesting magnetic behavior from reduced titanium dioxide nanobelts
Authors: Chong S. V. , Kadowaki K. , Xia J. , Idriss H.
Published: June 2008

The magnetic behavior of titanium dioxide nanobelts has been investigated with and without Co doping. Room temperature ferromagnetism was observed when the Co-doped anatase TiO2 nanobelts were prepared via vacuum annealing of 2.5at.% Co-doped titanate nanobelts, while annealing them in air resulted in paramagnetic ordering. Interestingly, by vacuum annealing the undoped titanate nanobelts under the same conditions, superparamagnetic ordering was observed in the resulting anatase TiO2 nanobelts. The electron paramagnetic resonance of this latter sample shows a strong symmetrical signal at g=2.003 suggesting some sort of exchange interactions among the localized electrons’ spin moments from single electron trapped in oxygen vacancies.
Dislocation network at InN∕GaN interface revealed by scanning tunneling microscopy
Authors: Liu Y. , Cai Y. , Zhang Lixin , Xie M. H. , Wang N. , Zhang S. B. , Wu H. S.
Published: June 2008

For heteroepitaxy of InN on GaN(0001) by molecular-beam epitaxy, the lattice misfit strain is relieved by misfit dislocations (MDs) formed at the interface between InN and GaN. Imaging by scanning tunneling microscopy (STM) of the surfaces of thin InN epifilms reveals line feature parallel to ⟨112¯0⟩. Their contrast becomes less apparent for thicker epifilms. From the interline spacing as well as a comparison with transmission electron microscopy studies, it is suggested that they correspond to the MDs beneath the surface. The STM contrast originates from both the surface distortion caused by the local strain at MDs and the electronic states of the defects.
Parallel laser printing of nanoparticulate silver thin film patterns for electronics
Authors: Shin Hyunkwon , Lee Hyeongjae , Sung Jinwoo , Lee Myeongkyu
Published: June 2008

This report discusses a parallel laser printing process for fabricating metallization patterns, which utilizes a pulsed laser-induced thermoelastic force exerting on nanoparticles. Silver thin films solution deposited on a glass substrate were transferred onto diverse receiver substrates such as Si, glass, and plastics by a spatially modulated Nd:YAG pulsed laser beam (1064nm, 6ns pulse width). High-fidelity patterns at the sub-10μm scales could be printed over several cm2 by a single pulse with 850mJ of energy. The fabrication of organic thin film transistors is demonstrated using printed source and drain Ag electrodes.
A black-box re-weighting analysis can correct flawed simulation data
Authors: Ytreberg F. Marty , Zuckerman Daniel M.
Published: June 2008

There is a great need for improved statistical sampling in a range of physical, chemical, and biological systems. Even simulations based on correct algorithms suffer from statistical error, which can be substantial or even dominant when slow processes are involved. Further, in key biomolecular applications, such as the determination of protein structures from NMR data, non-Boltzmann-distributed ensembles are generated. We therefore have developed the “black-box” strategy for reweighting a set of configurations generated by arbitrary means to produce an ensemble distributed according to any target distribution. In contrast to previous algorithmic efforts, the black-box approach exploits the configuration-space density
observed
in a simulation, rather than assuming a desired distribution has been generated. Successful implementations of the strategy, which reduce both statistical error and bias, are developed for a one-dimensional system, and a 50-atom peptide, for which the correct 250-to-1 population ratio is recovered from a heavily biased ensemble.
Stage-specific gene expression is a fundamental characteristic of rat spermatogenic cells and Sertoli cells
Authors: Johnston Daniel S. , Wright William W. , DiCandeloro Paul , Wilson Ewa , Kopf Gregory S. , Jelinsky Scott A.
Published: June 2008

Mammalian spermatogenesis is a complex biological process that occurs within a highly organized tissue, the seminiferous epithelium. The coordinated maturation of spermatogonia, spermatocytes, and spermatids suggests the existence of precise programs of gene expression in these cells and in their neighboring somatic Sertoli cells. The objective of this study was to identify the genes that execute these programs. Rat seminiferous tubules at stages I, II–III, IV–V, VI, VIIa,b, VIIc,d, VIII, IX–XI, XII, and XIII–XIV of the cycle were isolated by microdissection, whereas Sertoli cells, spermatogonia plus early spermatocytes, pachytene spermatocytes, and round spermatids were purified from enzymatically dispersed testes. Microarray analysis by using Rat Genome 230 2.0 arrays identified 16,971 probe sets that recognized testicular transcripts, and 398 of these were identified as testis-specific. Expression of 1,286 probe sets were found to differ at least 4-fold between two cell types and also across the stages of the cycle. Pathway and annotated cluster analyses of those probe sets predicted that entire biological pathways and processes are regulated cyclically in specific cells. Important among these are the cell cycle, DNA repair, and embryonic neuron development. Taken together, these data indicate that stage-regulated gene expression is a widespread and fundamental characteristic of spermatogenic cells and Sertoli cells.
Impact of an Environmental Cleaning Intervention on the Presence of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococci on Surfaces in Intensive Care Unit Rooms
Authors: Goodman Eric R. , Piatt Richard , Bass Richard , Onderdonk Andrew B. , Yokoe Deborah S. , Huang Susan S.
Published: June 2008

Objectives.

To evaluate the adequacy of discharge room cleaning and the impact of a cleaning intervention on the presence of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) on environmental surfaces in intensive care unit (ICU) rooms.

Design.

Prospective environmental study.

Setting and sample.

Convenience sample of ICU rooms in an academic hospital.

Methods and intervention.

The intervention consisted of (1) a change from the use of pour bottles to bucket immersion for applying disinfectant to cleaning cloths, (2) an educational campaign, and (3) feedback regarding adequacy of discharge cleaning. Cleaning of 15 surfaces was evaluated by inspecting for removal of a preapplied mark, visible only with an ultraviolet lamp (“black light”). Six surfaces were cultured for MRSA or VRE contamination. Outcomes of mark removal and culture positivity were evaluated by X2 testing and generalized linear mixed models, clustering by room.

Results.

The black-light mark was removed from 44% of surfaces at baseline, compared with 71 % during the intervention (P < .001). The intervention increased the likelihood of removal of black-light marks after discharge cleaning (odds ratio, 4.4; P < .001), controlling for ICU type (medical vs surgical) and type of surface. The intervention reduced the likelihood of an environmental culture positive for MRSA or VRE (proportion of cultures positive, 45% at baseline vs 27% during the intervention; adjusted odds ratio, 0.4; P = .02). Broad, flat surfaces were more likely to be cleaned than were doorknobs and sink or toilet handles.

Conclusions.

Increasing the volume of disinfectant applied to environmental surfaces, providing education for Environmental Services staff, and instituting feedback with a black-light marker improved cleaning and reduced the frequency of MRSA and VRE contamination.
Factors Associated with Recovery of Acinetobacter baumannii in a Combat Support Hospital
Authors: Griffith Matthew E. , Gonzalez Russell S. , Holcomb John B. , Hospenthal Duane R. , Wortmann Glenn W. , Murray Clinton K.
Published: June 2008

A retrospective review of hospital records for Acinetobacter baumannii infection at a US Army combat support hospital revealed a monthly infection rate ranging from 20.5 to 0 cases per 1,000 patients admitted. The rate correlated with the mean census of host-nation patients in the intensive care unit, the mean census of host-nation patients on the wards, and length of stay in the intensive care unit.
MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon
Authors: Park Yungki , Helms Volkhard
Published: June 2008

Summary: To be fully functional, membrane proteins should not only fold, but also get inserted into the membrane, which is mediated by the Sec61 translocon. Recent experimental studies have attempted to elucidate how the Sec61 translocon accomplishes this delicate task by measuring the translocon-mediated membrane insertion free energies of 357 systematically designed peptides. On the basis of this data set, we have developed MINS2, a novel sequence-based computational method for predicting the membrane insertion free energies of protein sequences. A benchmark analysis of MINS2 shows that MINS2 significantly outperforms previously proposed methods. Importantly, the application of MINS2 to known membrane protein structures shows that a better prediction of membrane insertion free energies does not lead to a better prediction of transmembrane segments of polytopic membrane proteins.

Availability: A web server for MINS2 is publicly available at http://service.bioinformatik.uni-saarland.de/mins.

Contact:  volkhard.helms@bioinformatik.uni-saarland.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
DNAlive: a tool for the physical analysis of DNA at the genomic scale
Authors: Goñi J. Ramon , Fenollosa Carlos , Pérez Alberto , Torrents David , Orozco Modesto
Published: June 2008

Summary: DNAlive is a tool for the analysis and graphical display of structural and physical characteristics of genomic DNA. The web server implements a wide repertoire of metrics to derive physical information from DNA sequences with a powerful interface to derive 3D information on large sequences of both naked and protein-bound DNAs. Furthermore, it implements a mesoscopic Metropolis code which allows the inexpensive study of the dynamic properties of chromatin fibers. In addition, our server also surveys other protein and genomic databases allowing the user to combine and explore the physical properties of selected DNA in the context of functional features annotated on those regions.

Availability:  http://mmb.pcb.ub.es/DNAlive/ ; http://www.inab.org/

Contact:  modesto@mmb.pcb.ub.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value
Authors: Boulesteix Anne-Laure , Porzelius Christine , Daumer Martin
Published: June 2008

Motivation: In the context of clinical bioinformatics methods are needed for assessing the additional predictive value of microarray data compared to simple clinical parameters alone. Such methods should also provide an optimal prediction rule making use of all potentialities of both types of data: they should ideally be able to catch subtypes which are not identified by clinical parameters alone. Moreover, they should address the question of the additional predictive value of microarray data in a fair framework.

Results: We propose a novel but simple two-step approach based on random forests and partial least squares (PLS) dimension reduction embedding the idea of pre-validation suggested by Tibshirani and colleagues, which is based on an internal cross-validation for avoiding overfitting. Our approach is fast, flexible and can be used both for assessing the overall additional significance of the microarray data and for building optimal hybrid classification rules. Its efficiency is demonstrated through simulations and an application to breast cancer and colorectal cancer data.

Availability: Our method is implemented in the freely available R package ‘MAclinical’ which can be downloaded from http://www.stat.uni-muenchen.de/~socher/MAclinical

Contact:  boulesteix@slcmsr.org
Detection and Molecular Characterization of Two Little Leaf Phytoplasma Strains Associated with Pepper and Tomato Diseases in Guanajuato and Sinaloa, Mexico
Authors: Santos-Cervantes M. E. , Chávez-Medina J. A. , Méndez-Lozano J. , Leyva-López N. E.
Published: June 2008

Pepper (Capsicum annuum) and tomato (Lycopersicon esculentum) are important vegetable crops in Mexico. Recently, symptoms associated with phytoplasma diseases such as witches'-broom (shoot proliferation) and little leaf were observed in pepper and tomato fields in central and northwestern Mexico. DNA extracted from symptomatic and asymptomatic plants was used in nested polymerase chain reaction (PCR) assays with primers amplifying 16S rDNA sequences for phytoplasmas. Twenty-four percent of pepper and 49% of tomato samples yielded a nested rDNA product of 1.25 kb. Restriction fragment length polymorphism profiles and sequencing of PCR products allowed classification of the detected phytoplasmas with the aster yellows group (16SrI). Both phytoplasmas, pepper little leaf (PeLL) and tomato little leaf (ToLL), could be included as new members of the aster yellows group because HaeIII and TaqI restriction enzymes discriminated among these phytoplasmas and members of other 16SrI subgroups. PeLL and ToLL phytoplasma sequences were deposited and compared with those in GenBank, and the maximum identity was found with several isolates of ‘Candidatus Phytoplasma asteris’. The highest identity (99%) has been observed with tomatillo little leaf phytoplasma and ash witches'-broom phytoplasma. This is the first report of ‘Ca. Phytoplasma asteris’ associated with pepper and tomato diseases in the Mexican states of Guanajuato and Sinaloa.
Influence of Cold-Hardening and Soil Matric Potential on Resistance to Speckled Snow Mold in Wheat
Authors: Nishio Zenta , Iriki Norio , Takata Kanenori , Ito Miwako , Tabiki Tadashi , Murray Timothy D.
Published: June 2008

The influence of soil matric potential, cold-hardening temperature, and duration on resistance to speckled snow mold caused by Typhula ishikariensis in wheat was investigated. Six winter wheat lines were subjected to cold-hardening temperatures of 2 or 4°C for 1, 2, 3, or 4 weeks with soil matric potential of –0.1 or –0.01 MPa. Plants were inoculated with T. ishikariensis after cold-hardening, incubated at 10°C for 25 days in the dark, and then evaluated for regrowth. Overall recovery from snow mold was least when plants were hardened at 2°C for 1 week at –0.01 MPa and greatest when hardened at 4°C for 4 weeks at –0.1 MPa. Survival of plants following snow mold was greater when plants were cold-hardened at 4 than at 2°C and at –0.1 than –0.01 MPa soil matric potential. The greatest difference in survival among lines and correlation with field observations occurred when plants were hardened at 4°C at –0.1 MPa matric potential for 3 weeks. Understanding the influence of temperature and soil matric potential during cold-hardening on speckled snow mold resistance will be useful to breeding programs developing snow-mold-resistant cultivars under controlled environment conditions.
A Strain ofClover yellow vein virusthat Causes Severe Pod Necrosis Disease in Snap Bean
Authors: Larsen Richard C. , Miklas Phillip N. , Eastwell Kenneth C. , Grau Craig R.
Published: June 2008

Soybean aphid (Aphis glycines) outbreaks occurring since 2000 have been associated with severe virus epidemics in snap bean (Phaseolus vulgaris) production in the Great Lakes region. Our objective was to identify specific viruses associated with the disease complex observed in the region and to survey bean germplasm for sources of resistance to the causal agents. The principle causal agent of the disease complex associated with extensive pod necrosis was identified as Clover yellow vein virus (ClYVV), designated ClYVV-WI. The virus alone caused severe mosaic, apical necrosis, and stunting. Putative coat protein amino acid sequence from clones of amplicons generated by reverse-transcription polymerase chain reaction was 98% identical to ClYVV strain no. 30 identified in Japan that has not been reported to cause pod necrosis. ClYVV-WI amplicons were 96% identical to a mild strain of ClYVV from Oregon. A distinguishing feature of this new strain is that it does not react with Potyvirus broad-spectrum monoclonal antibody PTY 1. A survey of common bean lines and cultivars revealed that, in addition to UI-31 and US1140 with known resistance to ClYVV, lines with the bc-3 gene for resistance to Bean common mosaic necrosis virus also were resistant to ClYVV-WI. An evaluation of 63 snap bean cultivars and breeding lines revealed just one, Roma 442, with a moderate level of tolerance to ClYVV-WI. Introgression of the bc-3 gene and resistances from UI-31 and US1140 into snap bean may offer a high level of resistance to extensive pod necrosis disease caused by ClYVV in the Great Lakes region.
A New Pathotype of Pepper mild mottle virus (PMMoV) Overcomes the L4 Resistance Genotype of Pepper Cultivars
Authors: Antignus Y. , Lachman O. , Pearlsman M. , Maslenin L. , Rosner A.
Published: June 2008

The biological, serological, and molecular characteristics of a newly isolated L4 resistance-breaking isolate of Pepper mild mottle virus (PMMoV) were studied. The new pathotype of PMMoV is closely related to the Israeli pathotypes P1,2 and P1,2,3 of the virus; however, the mosaic symptoms caused by this new pathotype on pepper plants with an L4 genotype were more severe than the mild mosaic symptoms caused by other common pathotypes of the virus in susceptible plants. The predicted amino acid sequence of the putative coat protein (CP) of the newly described pathotype has two amino acid mismatches when compared with the CP of pathotype P1,2, leucine to glutamine at position 47, and alanine to glycine at position 87. The CP of the new pathotype has one amino acid mismatch when compared with P1,2,3, having alanine instead of glycine at position 87. Based on its biological characteristics, the new pathotype was designated P1,2,3,4 of PMMoV-Is. A method is described for the differentiation among the three PMMoV pathotypes using restriction cleavage analysis of reverse-transcription polymerase chain reaction products made from virus-infected plants. An additional unique MnlI site in the CP gene of the newly isolated P1,2,3,4 allows its distinction from the other two isolates, while BglI cleaved only products of the P1,2 pathotype.
Relationships Between Oleic and Linoleic Acid Content and Seed Colonization by Cercospora kikuchii and Diaporthe phaseolorum
Authors: Xue H. Q. , Upchurch R. G. , Kwanyuen P.
Published: June 2008

Compared with standard cultivars, seed of mid-oleic soybean genotypes sometimes have shown increased colonization by Cercospora kikuchii in the field as judged by increased levels of purple-stained seed. To examine relationships between oleic and linoleic acid levels in soybean seed and postharvest seed colonization by two fungal seed pathogens, we inoculated seed with differing oleic:linoleic acid (O/L) ratios. Seed with defined O/L ratios were produced by allowing seed development of two isogenic soybean lines to occur in three different air temperature environments. Seed produced in these environments were harvested, individually analyzed for fatty acid composition, and inoculated with mycelium preparations of the fungal seed pathogens C. kikuchii or Diaporthe phaseolorum var. sojae. Fungal biomass of infected seed was quantified by measuring in vitro ergosterol content. For both soybean lines, colonization by C. kikuchii was positively correlated with the O/L ratio (r = 0.55, P < 0.03) and oleic acid content (r = 0.61, P < 0.02), and negatively correlated with linoleic (r = –0.60, P < 0.02) and linolenic (r = –0.58, P < 0.03) acid content. No association was found between the extent of seed colonization by D. phaseolorum and the seed O/L ratio. Our data suggest that the O/L ratio may be related to soybean seed colonization by C. kikuchii, but there is no evidence of a relationship with D. phaseolorum var. sojae colonization.
Suppression of Resistance-Breaking Beet necrotic yellow vein virus Isolates by Beet oak-leaf virus in Sugar Beet
Authors: Liu H.-Y. , Lewellen R. T.
Published: June 2008

Rhizomania, a serious disease of sugar beet (Beta vulgaris), is caused by Beet necrotic yellow vein virus (BNYVV). Resistance allele Rz1 has been widely incorporated into commercial cultivars. Recently, resistance-breaking isolates of BNYVV (RB-BNYVV) were identified and characterized. When the occurrence of RB-BNYVV was surveyed throughout the sugar-beet-growing areas in the United States, most soil samples contained Beet oak-leaf virus (BOLV) as well. BNYVV and BOLV often occurred in the same field and sometimes in the same sugar beet plant. The possibility of interactions between these two Polymyxa betae-transmitted sugar beet viruses was tested. Plants grown in soils infested with aviruliferous P. betae or carrying RB-BNYVV and BOLV, alone and in combination, were compared with plants grown in noninfested soil for differences in plant fresh weight and virus content as measured by enzyme-linked immunosorbent assay (ELISA). Rz1 and Rz2 resistance genes that condition resistance to BNYVV did not confer resistance to BOLV. BNYVV ELISA values were significantly higher in single infections than in mixed infections with BOLV in both the rhizomania-resistant and -susceptible cultivars. In contrast, ELISA values of BOLV were not significantly different between single and mixed infections in both the rhizomania-resistant and -susceptible cultivars. Results indicate that BOLV may suppress BNYVV in mixed infections. Soils infested with P. betae significantly reduced fresh weight of sugar beet seedlings regardless of whether they were with or without one or both viruses or resistance genes.
Control of Citrus Canker and Citrus Bacterial Spot with Bacteriophages
Authors: Balogh Botond , Canteros B. I. , Stall R. E. , Jones J. B.
Published: June 2008

Bacteriophages, alone or in combination with copper bactericides, were evaluated for managing Asiatic citrus canker and citrus bacterial spot incited by Xanthomonas axonopodis pathovars citri and citrumelo, respectively. In a set of five greenhouse experiments, phage treatment provided consistent control of citrus canker, causing an average of 59% reduction in disease severity. However, treatment with phage was ineffective if applied with skim milk, a protective formulation, which increases phage residual activity. In nursery settings, phage treatment also reduced disease but was less effective than copper-mancozeb, a chemical bactericide. The integration of phage and copper-mancozeb resulted in equal or less control than copper-mancozeb application alone. Phage treatments were evaluated in a commercial citrus nursery for reducing citrus bacterial spot caused by natural inoculum. Phage treatment provided significant disease reduction on moderately sensitive Valencia oranges in two trials (48 and 35%); however, on the highly susceptible grapefruit host it was ineffective. In an experimental citrus nursery, phage treatment provided significant control of citrus bacterial spot caused by a phage-sensitive strain, but was equally or less effective than copper-mancozeb. The combination of phage and copper-mancozeb did not increase control compared with copper-mancozeb alone.
Variation in Disease Incidence of Phomopsis Cane and Leaf Spot of Grape in Commercial Vineyards in Ohio
Authors: Nita M. , Ellis M. A. , Madden L. V.
Published: June 2008

A statewide survey for incidence of Phomopsis cane and leaf spot of grape (caused by Phomopsis viticola) was conducted during the 2002 to 2004 growing seasons. Over the 3 years, disease was observed in all surveyed vineyards, and mean disease incidence for leaves and internodes was 42 and 50%, respectively. A hierarchical linear mixed model was used to evaluate effects of region, farm within region, vineyard within farm, sampling site (i.e., vine) within vineyard, and shoot (i.e., cane) within vine on disease incidence. Region of the state did not have a significant effect on incidence but there was significant variation at all other levels of the hierarchy (P < 0.05); the greatest variation was at the lowest scale (shoots within vines). The potential effects of weather and management practices on disease risk at the vineyard scale were determined by using nonparametric correlation and binary logistic analyses after first classifying mean incidence per vineyard as being below or above 20% (D20 = 0,1) and 40% (D40 = 0,1). Overall results indicated that variables for predicted number of moderate infection events (DM; based on ambient temperature and hours when either there was measured rainfall or relative humidity above 90%), the extent of fungicide application (C) during early- and mid-May (M1 and M2, respectively), and the use of a dormant-period application of fungicide (DOR) were the key factors in predicting disease risk (for either D20 or D40). Accuracy (percentage of high and low disease vineyards correctly predicted) and area under the receiver operating characteristic curve (an overall measure of the accuracy of a model) for a generic model combining these predictor variables were 74 and 0.84, respectively, for D40 and 87 and 0.97, respectively, for D20. Models based on management practices were as accurate as those that incorporated weather variables. Although the degree of control of this disease is inadequate in Ohio, based on the survey results for incidence, the results from the risk-model analysis showed that improved management might be obtained by applying fungicide early during the growing season.
Pathotypes, Distribution, and Metalaxyl Sensitivity of Phytophthora sojae from North Dakota
Authors: Nelson B. D. , Mallik I. , McEwen D. , Christianson T.
Published: June 2008

Phytophthora root rot, caused by Phytophthora sojae, is the most important disease of soybean (Glycine max) in North Dakota. Because of the expansion of soybean hectares and appearance of disease on cultivars with resistance genes, we investigated the pathotypes, distribution, and metalaxyl sensitivity of P. sojae in North Dakota. Soil from 347 soybean fields in 20 counties in eastern North Dakota was collected between 2002 and 2004, and P. sojae was baited from the soil with the susceptible cultivar McCall. The virulence phenotype of each isolate was determined on eight differentials, and all isolates were tested for sensitivity to metalaxyl incorporated into V8 agar. The pathogen was recovered from 80 fields located in five counties. Sixteen pathotypes, which included 14 known races and two previously reported pathotypes that had not been assigned a race, were identified out of 157 isolates. A single pathotype was recovered from 61 fields, 2 pathotypes from 14 fields, 3 pathotypes from 4 fields, and 4 pathotypes from 1 field. Pathotypes with virulence phenotypes 1a,1c,7 (race 4; 39%) and 1a,7 (race 3; 28%) were the most common, representing 67% of the total isolates. One or both of these pathotypes was found in 79% of the fields where P. sojae was recovered. Seven of the 157 isolates showed limited growth on metalaxyl after 14 days of incubation. In the past 10 years, the number of pathotypes of P. sojae in North Dakota has increased from 4 to 16, and pathotypes have developed that can attack the three most common resistance genes found in soybean cultivars for the region.
Ontogenic Resistance to Uncinula necator Varies by Genotype and Tissue Type in a Diverse Collection of Vitis spp.
Authors: Gee Christopher T. , Gadoury David M. , Cadle-Davidson Lance
Published: June 2008

Berries of grapevine (Vitis spp.) have a limited window of susceptibility to Uncinula necator, the causal agent of grapevine powdery mildew, until the onset of ontogenic resistance approximately 2 to 3 weeks postbloom. This phenomenon has been demonstrated in several cultivars of V. vinifera and in V. labruscana ‘Concord’, which all exhibited a similar duration of susceptibility. To identify genetic variation for ontogenic resistance, we screened a diverse collection of Vitis species and interspecific hybrids maintained in the USDA-ARS cold-hardy Vitis germplasm collection in Geneva, NY. Of the 79 genotypes whose fruit clusters were screened for susceptibility to powdery mildew under field conditions, 50 exhibited a high level of constitutive resistance to powdery mildew and did not develop more than trace levels of disease when inoculated, irrespective of the stage of berry development at inoculation. Twenty-four genotypes exhibited a significant gain of resistance as berries aged. This ontogenic resistance was conserved across four species and several interspecific hybrids of Vitis spp., although the timing of the onset of ontogenic resistance varied by genotype. The mechanism of ontogenic resistance was examined for four genotypes. Similar to previous studies, ontogenic resistance greatly reduced the incidence of successful penetration. Despite the broad conservation of ontogenic resistance across species, one genotype (V. rupestris ‘R-65-44’) remained susceptible past the onset of ripening, over 1 month later than reported previously for V. vinifera and V. labruscana. Variation in the resistance phenotype was observed among the rachis, pedicels, and berries within clusters of the majority of genotypes studied. The genetic variation in ontogenic resistance, in particular the discovery of a genotype in which berries remain susceptible as they mature, will facilitate further study of the inheritance and molecular basis of ontogenic resistance.
Virulence Structure of the Eastern U.S. Wheat Powdery Mildew Population
Authors: Parks Ryan , Carbone Ignazio , Murphy J. Paul , Marshall David , Cowger Christina
Published: June 2008

Little is known about the population structure of wheat powdery mildew in the eastern United States, and the most recent report on virulence in this population involved isolates collected in 1993–94. In the present study, wheat leaves naturally infected with powdery mildew were collected from 10 locations in the southeastern United States in 2003 and 2005 and a collection of 207 isolates was derived from single ascospores. Frequencies of virulence to 16 mildew resistance (Pm) genes were determined by inoculating the isolates individually on replicated plates of detached leaves of differential wheat lines. These virulence frequencies were used to infer local effectiveness of Pm genes, estimate virulence complexity, detect significant associations between pairs of pathogen avirulence loci, and assess whether phenotypic differences between pathogen subpopulations increased with geographic distance. In both years, virulence to Pm3a, Pm3c, Pm5a, and Pm7 was present in more than 90% of sampled isolates and virulence to Pm1a, Pm16, Pm17, and Pm25 was present in fewer than 10% of isolates. In each year, 71 to 88% of all sampled isolates possessed one of a few multilocus virulence phenotypes, although there were significant differences among locations in frequencies of virulence to individual Pm genes. Several significant associations were detected between alleles for avirulence to pairs of Pm genes. Genetic (phenotypic) distance between isolate subpopulations increased significantly (R2 = 0.40, P < 0.001) with increasing geographic separation; possible explanations include different commercial deployment of Pm genes and restricted gene flow in the pathogen population.
Squash vein yellowing virus Detection Using Nested Polymerase Chain Reaction Demonstrates that the Cucurbit Weed Momordica charantia Is a Reservoir Host
Authors: Adkins Scott , Webb Susan E. , Baker Carlye A. , Kousik Chandrasekar S.
Published: June 2008

Squash vein yellowing virus (SqVYV) is a recently described ipomovirus from cucurbits in Florida that induces the relatively unusual symptoms in watermelon of plant death and fruit rind necrosis and discoloration, commonly known in Florida as watermelon vine decline. In this report, SqVYV infection of Momordica charantia (Balsam-apple), a common cucurbit weed, collected in 2005 and 2007 from within or adjacent to fields of declining watermelon, is demonstrated through the use of nested polymerase chain reaction (PCR). M. charantia plants located in or around fallow watermelon fields between spring and fall 2007 watermelon crops were also infected with SqVYV, indicating that this weed can serve as an oversummering host for this virus. Furthermore, whiteflies were able to acquire SqVYV from infected M. charantia and transmit it to squash and watermelon. Nested PCR was 10 to 1,000 times more sensitive than non-nested PCR for SqVYV detection in several cucurbit hosts, including M. charantia and watermelon. Melothria pendula (creeping cucumber), another common cucurbit weed, was experimentally infected with SqVYV. These results suggest that improved management of M. charantia and other cucurbit weeds needs to be incorporated into watermelon vine decline management plans to reduce sources of SqVYV and other cucurbit viruses.
Detection, Quantification, and Vegetative Compatibility of Verticillium dahliae in Potato and Mint Production Soils in the Columbia Basin of Oregon and Washington
Authors: Omer M. A. , Johnson D. A. , Douhan L. I. , Hamm P. B. , Rowe R. C.
Published: June 2008

Soil samples from 87 fields intended for potato production in the Columbia Basin of Washington and Oregon and 51 fields intended for mint production in Washington were assayed on a semiselective medium to quantify populations of Verticillium dahliae. The pathogen was isolated from 77 (89%) of the fields intended for potato production and 41 (80%) of the fields intended for mint production. Population densities ranged from 0 to 169 propagules/g of air-dried soil in fields intended for potato production and 0 to 75 propagules/g of air-dried soil in fields intended for mint production. Isolates of V. dahliae were recovered from soil assay plates and pure cultures were prepared to provide a collection of isolates for vegetative compatibility analysis. Among fields intended for potato production from which isolates of the fungus were assigned to a vegetative compatibility group (VCG), 93% of the fields were found to contain one or more isolates assigned to VCG 4A, nine (23%) contained one or more isolates assigned to VCG4B, and only one (3%) contained any isolates assigned to VCG 2B. In the case of fields planned for mint production in 1999 from which isolates of the fungus were assigned to a VCG, 13 fields (81%) were found to contain one or more isolates assigned to VCG 4A, 7 (44%) contained one or more isolates assigned to VCG 4B, and 5 (31%) contained one or more isolates assigned to VCG 2B. VCG 4A isolates of V. dahliae are widespread and numerous, particularly following potato production, but cause only mild to moderate symptoms in mint; therefore, this pathotype is unlikely to seriously endanger subsequent plantings of mint. However, planting potato in a field recently used to produce mint may pose a significant risk to the potato crop if high populations of the VCG4A pathotype (highly aggressive to potato) predominate. Preplant assessment of soil populations of V. dahliae without regard for the relative populations of various pathotypes present in a particular sample may lead to information not fully useful in integrated pest management systems.
First Report of Lethal Yellowing Group (16Sr IV) of Phytoplasmas in Vernonia cinerea in Jamaica
Authors: Brown S. E. , Been B. O. , McLaughlin W. A.
Published: June 2008

Coconut lethal yellowing disease (CLY) has had a devastating effect on the coconut (Cocos nucifera L.) industry in Jamaica and Latin America. A study was conducted in Jamaica during 2005 to identify alternate hosts of the CLY phytoplasma. Since weeds are known to act as reservoir hosts of numerous pathogens, Vernonia cinerea (L.) (Asteraceae), a prevalent weed species on coconut farms island-wide, was collected from coconut farms in areas of high and low levels of CLY incidence, although none of the plants displayed disease symptoms. DNA was extracted from plant samples by the method of Dellaporta et al. (1) and analyzed by nested PCR assay employing phytoplasma universal rRNA operon primers P1/P7 (2,4) and LY16Sf/LY16-23Sr (3). DNA derived from CLY-diseased or healthy coconut palm served as positive and negative controls, respectively, in each assay. Amplification of an rDNA product of the expected size (1.7 kb) confirmed phytoplasma infections in 53 of 118 (44.9%) V. cinerea test plants. Twenty-seven of the rDNA PCR products were analyzed by digestion with restriction enducleases RsaI, MspI, MseI, TaqI, HinfI, and HhaI. The restriction fragment length polymorphism profiles obtained were similar to that observed in the CLY-infected coconut palm. V. cinerea rDNA amplicons were cloned and sequenced (in both directions) and a representative sequence was deposited in GenBank (Accession No. EU057983). Blast analysis determined this sequence to be most similar (99%) to that of CLY phytoplasma in Jamaica (Accession No. AF49807) and Florida (Accession No. AF498309). To our knowledge, this is the first report of the 16Sr IV group of phytoplasmas infecting V. cinerea. Presence of the lethal yellowing phytoplasmas in dicotyledonous plant species has important epidemiological implications concerning vector identity and ecology. Futhermore, it is now evident that weed control on coconut farms could assist in the management of CLY disease in Jamaica.

References: (1) S. L. Dellaporta et al. Plant Mol. Biol. Rep. 1:19, 1993. (2) S. Deng and C. Hiruki. J. Microbiol. Methods 14:53, 1991. (3) N. A. Harrison et al. Ann. Appl. Biol. 141:183, 2002. (4) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996.
First Report of Alfalfa mosaic virus in Viburnum lucidum in Spain
Authors: Cebrián M. C. , Córdoba-Sellés M. C. , Alfaro-Fernández A. , Herrera-Vásquez J. A. , Jordá C.
Published: June 2008

Viburnum sp. is an ornamental shrub widely used in private and public gardens. It is common in natural wooded areas in the Mediterranean Region. The genus includes more than 150 species distributed widely in climatically mild and subtropical regions of Asia, Europe, North Africa, and the Americas. In January 2007, yellow leaf spotting in young plants of Viburnun lucidum was observed in two ornamental nurseries in the Mediterranean area of Spain. Symptoms appeared sporadically depending on environmental conditions but normally in cooler conditions. Leaf tissue from 24 asymptomatic and five symptomatic plants was sampled and analyzed by double-antibody sandwich (DAS)-ELISA with specific polyclonal antibodies against Tomato spotted wilt virus (TSWV) (Loewe Biochemica, Sauerlach, Germany) and Alfalfa mosaic virus (AMV) (SEDIAG S.A.S, Longvic, France). All symptomatic plants of V. lucidum were positive for Alfalfa mosaic virus (AMV). The presence of AMV was tested in the 29 samples by one-step reverse transcription (RT)-PCR with the platinum Taq kit (Invitrogen Life Technologies, Barcelona, Spain) using primers derived from a partial fragment of the coat protein gene of AMV (2). The RT-PCR assays produced an expected amplicon of 700 bp in the five symptomatic seropositive samples. No amplification product was observed when healthy plants or a water control were used as a template in the RT-PCR assays. One PCR product was purified (High Pure PCR Product Purification Kit; Roche Diagnostics, Mannheim, Germany) and directly sequenced (GenBank Accession No. EF427449). BLAST analysis showed 96% nucleotide sequence identity to an AMV isolate described from Phlox paniculata in the United States (GenBank Accession No. DQ124429). This virosis has been described as affecting Viburnum tinus L. in France (1). To our knowledge, this is the first report of natural infection of Viburnum lucidum with AMV in Spain, which might have important epidemiological consequences since V. lucidum is a vegetatively propagated ornamental plant.

References: (1) L. Cardin et al. Plant Dis. 90:1115, 2006. (2) Ll. Martínez-Priego et al. Plant Dis. 88:908, 2004.