bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of Indeterminacies in Corrected ECG Signals Using Parameterized Multidimensional Independent Component Analysis
Authors: Chawla M. P. S.
Published: February 2009

Independent component analysis (ICA) is a new technique suitable for separating independent components from electrocardiogram (ECG) complex signals. The basic idea of using multidimensional independent component analysis (MICA) is to find stable higher dimensional source signal subspaces and to decompose each rotation into elementary rotations within all two‐dimensional planes spanned by the coordinate axes useful for diagnostic information of heart. In this paper, ability of ICA for parameterization of ECG signals was felt to reduce the amount of redundant ECG data. This work aims at finding an independent subspace analysis (ISA) model for ECG analysis that allows applicability to any random vectors available in an ECG data set. For the common standards for electrocardiography (CSE) based ECG data sets, joint approximate diagonalization of eigen matrices (Jade) algorithm is used to find smaller subspaces. The extracted independent components are further cleaned by statistical measures. In this study, it is also observed that the value of kurtosis coefficients for the independent components, which represents the noise component, can be further reduced using parameterized multidimensional ICA (PMICA) technique. The indeterminacies if available in the ECG data are to be analysed also using modified version of Jade algorithm to PMICA and parameterized standard ICA (PsICA) for comparative studies. The indeterminacies if available in the ECG data are reduced in PMICA better in comparison to the analysis done using PsICA. The simulation results obtained indicate that ICA definitely improves signal–noise ratio (SNR) like the other higher order digital filtering methods like Kalman, Butterworth etc. with minimum reconstruction errors. Here, it is also confirmed that re‐parameterization of the standard ICA model results into a ‘component model’ using MICA technique, which is geometric in spirit and free of indeterminacies existing in sICA model.
Theoretical Models for the Quantification of Lung Injury Using Ventilation and Perfusion Distributions
Authors: Brook B. S. , Murphy C. M. , Breen D. , Miles A. W. , Tilley D. G. , Wilson A. J.
Published: February 2009

This paper describes two approaches to modelling lung disease: one based on a multi‐compartment statistical model with a log normal distribution of ventilation perfusion ratio () values; and the other on a bifurcating tree which emulates the anatomical structure of the lung. In the statistical model, the distribution becomes bimodal, when the values of a randomly selected number of compartments are reduced by 85% to simulate lung disease. For the bifurcating tree model a difference in flow to the left and right branches coupled with a small random variation in flow ratio between generations results in a log normal distribution of flows in the terminal branches. Restricting flow through branches within the tree to simulate lung disease transforms this log normal distribution to a bi‐modal one. These results are compatible with those obtained from experiments using the multiple inert gas elimination technique, where log normal distributions of ratio become bimodal in the presence of lung disease.
Joint Probability‐Based Neuronal Spike Train Classification
Authors: Chen Yan , Marchenko Vitaliy , Rogers Robert F.
Published: February 2009

Neuronal spike trains are used by the nervous system to encode and transmit information. Euclidean distance‐based methods (EDBMs) have been applied to quantify the similarity between temporally‐discretized spike trains and model responses. In this study, using the same discretization procedure, we developed and applied a joint probability‐based method (JPBM) to classify individual spike trains of slowly adapting pulmonary stretch receptors (SARs). The activity of individual SARs was recorded in anaesthetized, paralysed adult male rabbits, which were artificially‐ventilated at constant rate and one of three different volumes. Two‐thirds of the responses to the 600 stimuli presented at each volume were used to construct three response models (one for each stimulus volume) consisting of a series of time bins, each with spike probabilities. The remaining one‐third of the responses where used as test responses to be classified into one of the three model responses. This was done by computing the joint probability of observing the same series of events (spikes or no spikes, dictated by the test response) in a given model and determining which probability of the three was highest. The JPBM generally produced better classification accuracy than the EDBM, and both performed well above chance. Both methods were similarly affected by variations in discretization parameters, response epoch duration, and two different response alignment strategies. Increasing bin widths increased classification accuracy, which also improved with increased observation time, but primarily during periods of increasing lung inflation. Thus, the JPBM is a simple and effective method performing spike train classification.
Christian Ungermann: Taking apart vacuole fusion
Authors: Short Ben
Published: February 2009

Christian Ungermann dissects the many steps involved in membrane trafficking.
FRANz: reconstruction of wild multi-generation pedigrees
Authors: Riester Markus , Stadler Peter F. , Klemm Konstantin
Published: February 2009

Summary: We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical dataset with known pedigree. The parentage inference is robust even in the presence of genotyping errors.

Availability: The C source code of FRANz can be obtained under the GPL from http://www.bioinf.uni-leipzig.de/Software/FRANz/.

Contact:  markus@bioinf.uni-leipzig.de
Overexpression of Brassica napus MPK4 Enhances Resistance to Sclerotinia sclerotiorum in Oilseed Rape
Authors: Wang Zheng , Mao Han , Dong Caihua , Ji Ruiqin , Cai Li , Fu Hao , Liu Shengyi
Published: February 2009

Sclerotinia sclerotiorum causes a highly destructive disease in oilseed rape (Brassica napus) resulting in significant economic losses. Studies on the Arabidopsis thaliana MPK4 loss-of-function mutant have implicated that AtMPK4 is involved in plant defense regulation, and its effect on disease resistance varies in different plant–pathogen interactions. In this study, we isolated a B. napus mitogen-activated protein kinase, BnMPK4, and found that BnMPK4 along with PDF1.2 are inducible in resistant line Zhongshuang9 but both are consistently suppressed in susceptible line 84039 after inoculation with S. sclerotiorum. Transgenic oilseed rape overexpressing BnMPK4 markedly enhances resistance to S. sclerotiorum and Botrytis cinerea. Further experiments showed that transgenic plants inhibited growth of S. sclerotiorum and constitutively activated PDF1.2 but decreased H2O2 production and constitutively suppressed PR-1 expression. Treatment of roots of the transgenic plants with H2O2 solution resulted in enhanced susceptibility to the two pathogens. Our results support the idea that MPK4 positively regulates jasmonic acid-mediated defense response, which might play an important role in resistance to S. sclerotiorum in oilseed rape.
Tomato Transcriptional Responses to a Foliar and a Vascular Fungal Pathogen Are Distinct
Authors: van Esse H. Peter , Fradin Emilie F. , de Groot Philip J. , de Wit Pierre J. G. M. , Thomma Bart P. H. J.
Published: February 2009

Plant activation of host defense against pathogenic microbes requires significant host transcriptional reprogramming. In this study, we compared transcriptional changes in tomato during compatible and incompatible interactions with the foliar fungal pathogen Cladosporium fulvum and the vascular fungal pathogen Verticillium dahliae. Although both pathogens colonize different host tissues, they display distinct commonalities in their infection strategy; both pathogens penetrate natural openings and grow strictly extracellular. Furthermore, resistance against both pathogens is conveyed by the same class of resistance proteins, the receptor-like proteins. For each individual pathogen, the expression profile of the compatible and incompatible interaction largely overlaps. However, when comparing between the two pathogens, the C. fulvum-induced transcriptional changes show little overlap with those induced by V. dahliae. Moreover, within the subset of genes that are regulated by both pathogens, many genes show inverse regulation. With pathway reconstruction, networks of tomato genes implicated in photorespiration, hypoxia, and glycoxylate metabolism were identified that are repressed upon infection with C. fulvum and induced by V. dahliae. Similarly, auxin signaling is differentially affected by the two pathogens. Thus, differentially regulated pathways were identified with novel strategies that allowed the use of state-of-the-art tools, even though tomato is not a genetic model organism.
The Zur of Xanthomonas campestris Is Involved in Hypersensitive Response and Positively Regulates the Expression of the hrp Cluster Via hrpX But Not hrpG
Authors: Huang Dong-Liang , Tang Dong-Jie , Liao Qing , Li Xiao-Qian , He Yong-Qiang , Feng Jia-Xun , Jiang Bo-Le , Lu Guang-Tao , Tang Ji-Liang
Published: February 2009

In bacteria, Zur is a key regulator for zinc homeostasis. Our previous work has shown that, in the phytopathogen Xanthomonas campestris pv. campestris, in addition to regulating zinc homeostasis, Zur is essential for full virulence. Here, we demonstrate that the X. campestris pv. campestris Zur is involved in hypersensitive response (HR) and positively regulates the transcription of hrpA to hrpF operons and hrpX but not hrpG. Constitutively expressing hrpX but not hrpG in the zur mutant could bypass the requirement of Zur for the expression of hrpA to hrpF operons and the induction of wild-type HR, indicating that Zur controls the expression of hrp cluster via hrpX. Promoter-gusA reporter and semiquantitative reverse-transcription polymerase chain reaction analyses revealed that HrpG controls the expression of hrpX and HrpX regulates the expression of all the six hrp operons (hrpA to hrpF) in X. campestris pv. campestris.
A Secreted SPRY Domain-Containing Protein (SPRYSEC) from the Plant-Parasitic NematodeGlobodera rostochiensisInteracts with a CC-NB-LRR Protein from a Susceptible Tomato
Authors: Rehman Sajid , Postma Wiebe , Tytgat Tom , Prins Pjotr , Qin Ling , Overmars Hein , Vossen Jack , Spiridon Laurentiu-N. , Petrescu Andrei-J. , Goverse Aska , Bakker Jaap , Smant Geert
Published: February 2009

Esophageal gland secretions from nematodes are believed to include effectors that play important roles in plant parasitism. We have identified a novel gene family encoding secreted proteins specifically expressed in the dorsal esophageal gland of Globodera rostochiensis early in the parasitic cycle, and which contain the B30.2/SPRY domain. The secondary structure of these proteins, named the secreted SPRY domain-containing proteins (SPRYSEC), includes highly conserved regions folding into β-strands interspersed with loops varying in sequence and in length. Mapping sequence diversity onto a three-dimensional structure model of the SPRYSEC indicated that most of the variability is in the extended loops that shape the so-called surface A in the SPRY domains. Seven of nine amino acid sites subjected to diversifying selection in the SPRYSEC are also at this surface. In both yeast-two-hybrid screening using a library from a susceptible tomato and in an in vitro pull-down assay, one of the SPRYSEC interacted with the leucine-rich repeat (LRR) region of a novel coiled-coil nucleotide-binding LRR protein, which is highly similar to members of the SW5 resistance gene cluster. Given that the tomato cultivar used is susceptible to nematode infection, this SPRYSEC could be an evolutionary intermediate that binds to a classical immune receptor but does not yet, or no longer, triggers a resistance response. Alternatively, this SPRYSEC may bind to the immune receptor to downregulate its activity.
Changes in Disease Resistance Phenotypes Associated With Plant Physiological Age Are Not Caused by Variation in R Gene Transcript Abundance
Authors: Millett Benjamin P. , Mollov Dimitre S. , Iorizzo Massimo , Carputo Domenico , Bradeen James M.
Published: February 2009

Foliar late blight is one of the most important diseases of potato. Foliar blight resistance has been shown to change as a plant ages. In other pathosystems, resistance (R) gene transcript levels appear to be correlated to disease resistance. The cloning of the broad-spectrum, foliar blight resistance gene RB provided the opportunity to explore how foliar blight resistance and R-gene transcript levels vary with plant age. Plants of Solanum bulbocastanum PT29, from which RB, including the native promoter and other flanking regions, was cloned, and S. tuberosum cv. Dark Red Norland (nontransformed and RB-transformed) representing three different developmental stages were screened for resistance to late blight and RB transcript levels. Preflowering plants of all genotypes exhibited the highest levels of resistance, followed by postflowering and near-senescing plants. The RB transgene significantly affected resistance, enhancing resistance levels of all RB-containing lines, especially in younger plants. RB transgene transcripts were detected at all plant ages, despite weak correlation with disease resistance. Consistent transcript levels in plants of different physiological ages with variable levels of disease resistance demonstrate that changes in disease-resistance phenotypes associated with plant age cannot be attributed to changes in R-gene transcript abundance.
Re-evaluation of Phytophthora Species Isolated During 30 Years of Vegetation Health Surveys in Western Australia Using Molecular Techniques
Authors: Burgess Treena I. , Webster Janet L. , Ciampini Juanita A. , White Diane , Hardy Giles E. StJ. , Stukely Michael J. C.
Published: February 2009

For 30 years, large-scale aerial photography has been used to map the extent of Phytophthora dieback disease in native forests in the southwest of Western Australia, with validation of the observations involving routine testing of soil and root samples for the presence of Phytophthora cinnamomi. In addition to P. cinnamomi, six morpho-species have been identified using this technique: P. citricola, P. megasperma, P. cryptogea, P. drechsleri, P. nicotianae, and P. boehmeriae. In recent years, many new Phytophthora species have been described worldwide, often with similar morphology to existing species; thus, as many of the isolates collected in Western Australia have been difficult to identify based on morphology, molecular identification of the morpho-species is required. Based on amplification of the internal transcribed spacer (ITS) region of the rDNA gene, sequence data of more than 230 isolates were compared with those of existing species and undescribed taxa. P. inundata, P. asparagi, P. taxon PgChlamydo, P. taxon personii, and P. taxon niederhauserii were identified based on sequence data. Phylogenetic analysis revealed that nine potentially new and undescribed taxa can be distinguished. Several of the new taxa are morphologically indistinguishable from species such as P. citricola, P. drechsleri, and P. megasperma. In some cases, the new taxa are closely related to species with similar morphology (e.g., P.sp.4 and P. citricola). However, the DNA sequences of other new taxa such as P.sp.3 and P.sp.9 show that they are not closely related to morphologically similar species P. drechsleri and P. megasperma, respectively. Most of the new taxa have been associated with dying Banksia spp., while P.sp.2 and P.sp.4 have also been isolated from dying Eucalyptus marginata (jarrah). Some taxa (P.sp.3, 6, and 7) appear to have limited distribution, while others like P.sp.4 are widespread.
Distribution of Mating Type and Sexual Status in Chinese Rice Blast Populations
Authors: Zeng Jing , Feng Shujie , Cai Jiangqiao , Wang Ling , Lin Fei , Pan Qinghua
Published: February 2009

A collection of 520 field isolates of the rice blast fungus (Magnaporthe oryzae) originating from five provinces in China was assessed for mating type and sexual fertility. One of the two tester sets was composed of isolates collected from barley and the other from rice. Two mating types (MAT1-1 and MAT1-2) were identified among the 443 fertile isolates. The two mating types were roughly in balance with one another in the southwestern region but one or the other predominated in the southeastern and southern regions. Male-only fertile isolates were the most common, and only a few hermaphroditic and no female only fertile isolates were detected. The fertility level of the isolates was variable. Isolates from Jiangsu were more fertile than those from Fujian. The mating capacity of the testers collected from barley was higher than that of those collected from rice, but this was because the MAT1-2 testers differed very significantly from one another. In contrast, the mating capacities of the two MAT1-1 testers were similar to one another.
Dieback and Mortality of Alnus in the Southern Rocky Mountains, USA
Authors: Worrall James J.
Published: February 2009

Dieback and mortality of Alnus incana subsp. tenuifolia in the Southern Rocky Mountains apparently began by the late 1980s and have become a concern to land managers. A survey of alder including 68 transects from southern Wyoming to northern New Mexico indicated that, of 6,503 standing stems, 37% were dead, 29% had dieback, and 34% were healthy. Transects intercepted 1,479 m of live and 1,177 m of dead alder canopy. A second, more localized survey with 32 transects in the upper Gunnison River watershed of Colorado yielded similar results. Abundance of live sprouts was inversely related to amount of dieback and mortality in a genet, suggesting that affected genets are dying and not replacing themselves. Damage did not vary substantially by geographic area and was not related to elevation, animal browsing, or distance to nearest road. Distance to nearest stream was weakly, inversely related to severity of dieback and mortality. Symptoms were not consistent with disease of alder caused by Phytophthora alni in Europe, and isolations for Phytophthora species were negative. Cytospora canker, caused by Valsa melanodiscus (anamorph Cytospora umbrina), is the proximate cause of the dieback and mortality.
Effect of a Chromosome Segment Marked by the Php Gene for Resistance to Phytophthora nicotianae on Reproduction of Tobacco Cyst Nematodes
Authors: Johnson C. S. , Wernsman E. A. , LaMondia J. A.
Published: February 2009

Host resistance is an important strategy for managing Globodera tabacum subsp. solanacearum and G. tabacum subsp. tabacum, important nematode pests of flue-cured tobacco (Nicotiana tabacum) in Virginia, and cigar wrapper tobacco (N. tabacum) in Connecticut and Massachusetts, respectively. Field research from 1992 to 2005 evaluated reproduction of G. tabacum subsp. solanacearum on genotypes with and without a chromosome segment from N. plumbaginifolia containing a gene (Php) that conferred resistance to race 0 of Phytophthora nicotianae (causal agent of tobacco black shank). Ratios of G. tabacum subsp. solanacearum eggs/500 cm3 soil at the end versus the beginning of experiments (Pf/Pi) were significantly lower in cultivars and breeding lines possessing the Php-containing chromosome segment from N. plumbaginifolia compared with genotypes without the segment. Numbers of vermiform G. tabacum subsp. solanacearum juveniles in roots were similar among genotypes but numbers of swollen and pyriform nematodes were significantly lower for the known G. tabacum subsp. solanacearum resistant cv. NC 567 and in genotypes possessing the Php gene compared with genotypes and cultivars without the gene. In a 2003 greenhouse test, the percentage of plants with visible G. tabacum subsp. tabacum cysts was also significantly lower for parental and progeny genotypes homozygous and heterozygous, respectively, for Php compared with similar lines without the gene. These results indicate a close linkage or association between a likely single, dominant gene (Php) for resistance to P. nicotianae and suppressed reproduction by G. tabacum subsp. solanacearum and G. tabacum subsp. tabacum. Further research to accurately elucidate the relationships among these genes could lead to significant improvements in tobacco disease control.
First Report of Powdery Mildew (Oidium sp.) on Pincushion Flower (Scabiosa columbaria) in New York
Authors: Jankovics T. , Kiss L. , Niks R. E. , Daughtrey M. L.
Published: February 2009

Scabiosa columbaria (Dipsacaceae) is a popular perennial ornamental in the United States. It is native to Europe and was introduced to North America by nursery trade only recently. In the spring of 2006, symptoms of powdery mildew infection were observed on overwintered plants of S. columbaria cv. Butterfly Blue in a nursery in Cutchogue, NY. White powdery mildew mycelia with abundant sporulation were observed on upper and lower leaf surfaces. The portions of leaves with powdery mildew colonies often showed purplish discoloration. Conidia were cylindric to doliiform, measured 20 to 33 × 10 to 15 μm, and were produced singly on 60 to 130 μm long conidiophores consisting of a foot-cell measuring 20 to 50 × 6 to 10 μm, followed by one to three, 12 to 40 μm long cells. Hyphal appressoria were lobed or multilobed. The teleomorph stage was not found. On the basis of these characteristics, the pathogen was identified as an Oidium sp. belonging to the subgenus Pseudoidium. Recently, an anamorphic powdery mildew fungus with similar morphological characteristics, identified as Erysiphe knautiae, was reported on S. columbaria cv. Butterfly Blue in Washington (2). E. knautiae is a common powdery mildew species of dipsacaceous plants such as Scabiosa spp. and Knautia spp. in Europe and Asia (1). To determine whether the fungus reported here was E. knautiae, DNA was extracted from its mycelium, and the internal transcribed spacer (ITS) region of the ribosomal DNA was amplified and sequenced as described earlier (4). No ITS sequences are available in public DNA databases for E. knautiae, thus, we determined this sequence in a specimen of E. knautiae collected from Knautia arvensis in The Netherlands. Herbarium specimens of the Oidium sp. infecting S. columbaria in New York and E. knautiae from the Netherlands were deposited at the U.S. National Fungus Collections under accession numbers BPI 878259 and BPI 878258, respectively. The ITS sequence from Oidium sp. infecting S. columbaria in New York (GenBank Accession No. EU377474) differed in two nucleotides from that of E. knautiae infecting K. arvensis in the Netherlands (GenBank Accession No. EU377475). These two ITS sequences were also more than 99% similar to those of some newly emerged anamorphic powdery mildew fungi: Oidium neolycopersici and other Oidium spp. infecting Chelidonium majus, Passiflora caerulea, and some crassulaceous plants (3,4). Thus, it is unclear whether the fungus reported here was E. knautiae known from Eurasia or an Oidium sp. that has acquired pathogenicity to S. columbaria. To our knowledge, this is the first report of powdery mildew on S. columbaria in New York.

References: (1) U. Braun. Beih. Nova Hedwigia 89:1, 1987. (2) D. A. Glawe and G. G. Grove. Online publication. doi:10.1094/PHP-2005-1024-01-BR. Plant Health Progress, 2005. (3) B. Henricot. Plant Pathol. 57:779, 2008. (4) T. Jankovics et al. Phytopathology 98:529, 2008.
First Report of Brown Root Rot of Alfalfa Caused by Phoma sclerotioides in Maine, Ontario, and Pennsylvania
Authors: Wunsch M. J. , Kersbergen R. , Tenuta A. U. , Hall M. H. , Bergstrom G. C.
Published: February 2009

Brown root rot (BRR), caused by the fungal pathogen Phoma sclerotioides G. Preuss ex Sacc. (synonym Plenodomus meliloti Dearn. & G.B. Sanford), is associated with yield loss of alfalfa (Medicago sativa L.) in regions with severe winters (1). In the spring of 2007, 9 to 69 alfalfa plants were collected from each of five production fields in Maine, 10 fields in Ontario, and nine fields in Pennsylvania. All alfalfa stands existed at least two winters. P. sclerotioides was isolated from alfalfa root and crown lesions from five fields in Maine (Penobscot, Somerset and Waldo counties), seven fields from southwestern (Woodstock and Niagara), south-central (Lindsay and Belleville), and southeastern Ontario (near Ottawa), and four fields in Pennsylvania (Columbia, Crawford, and Jefferson counties; 41.1 to 41.6°N). BRR incidence was 9 to 29% in Maine, 5 to 29% in Ontario, and 8 to 22% in Pennsylvania. In Ontario, some lesions girdled the crown; in three fields in Maine, large pycnidia characteristic of P. sclerotioides were present on alfalfa crowns and overwintered stems. On potato dextrose agar, conidia (5 to 8 × 2 to 3 μm, unicellular, hyaline, and ovoid) and pycnidia (0.33 to 1.15 mm in diameter with multiple beaks) of single-conidium isolates were characteristic of P. sclerotioides (2). Diagnostic PCR (3) of isolates resulted in a single amplicon of expected size (500 bp). The internal transcribed spacer (ITS) 1, 5.8S, and ITS2 of the rDNA were sequenced for 12 representative isolates, and sequences (GenBank Accession Nos. FJ179151 to FJ179162) were 95.5 to 100% identical to P. sclerotioides ATCC isolate 56515 over a 488-bp alignment. Eight months after seeding, potted ‘Vernal’ alfalfa was inoculated (4), kept at 4°C for 8 weeks, 0 to –2°C for 12 weeks, 4°C for 8 weeks, and 10 to 15°C for 7 weeks. Of 108 plants inoculated with the Maine isolates, 35 developed severe cortical lesions and 16 died. Of 18 plants inoculated with the Ontario isolates, 16 developed severe cortical lesions and eight died. Of 18 plants inoculated with a Pennsylvania isolate, 11 developed severe cortical lesions and five died. Lesions were typical of BRR: light to very dark brown, sometimes with a darker border, and often containing abundant pycnidia. Plant mortality was associated with lesions that girdled the root and crown. Of 18 plants in the control treatment, three developed severe cortical lesions and none died. BRR is common in Alberta, Saskatchewan, and Manitoba, but in eastern Canada it has been reported only in Nova Scotia. To our knowledge, this is the first report of BRR in Maine, Ontario, and Pennsylvania and the southernmost report of BRR in eastern North America.

References: (1) B. Berkenkamp et al. Can. J. Plant Sci. 71:211, 1991. (2) G. H. Boerema et al. Persoonia 15:431, 1994. (3) R. C. Larsen et al. Plant Dis. 86:928, 2002. (4) M. J. Wunsch et al. Plant Dis. 91:1293, 2007.
First Report of Downy Mildew on Nursery-Grown Hellebore Caused by Peronospora pulveracea in California
Authors: Warfield C. Y. , Blomquist C. L. , Lovig E. E.
Published: February 2009

Hellebore or Lenten rose (Helleborus × hybridus) is an evergreen, herbaceous perennial in the family Ranunculaceae. Hellebores are sold as decorative, potted plants and as shade-loving landscape plants favored for their attractive and prolonged blooms in late winter or early spring. In April of 2008, downy mildew-like growth was observed on the foliage of approximately 60 containerized plants of Helleborus ‘Blue Lady’, ‘Pink Lady’, ‘White Lady’, and ‘Royal Heritage’ grown outdoors in a retail nursery in coastal San Mateo County, California. Infected foliage had angular, vein-delimited, dark brown-to-black speckled lesions on adaxial leaf surfaces turning dry and necrotic with age. Young leaves were small and distorted. Affected flowers were spotted and brown. The abaxial sides of affected leaves had light brown-to-purplish downy mildew-like growth. Subhyaline conidia, globose to ellipsoid in shape, ranged from 25 to 31 × 17 to 24 μm (average 28 × 21 μm). Conidiophores ranged from 265 to 375 × 5 to 11.5 μm (average 333 × 8.9 μm), branching dichotomously four to five times in the upper half. Morphological measurements fell within the range previously described for Peronospora pulveracea and P. alpicola, which were reported on Helleborus spp. and Ranunculus aconitifolius, respectively (1,2). DNA sequence of the internal transcribed spacer region of rDNA of our isolate (Genbank Accession No. FJ384778) matched sequences of P. pulveracea (Genbank Accession No. AY198270) and P. alpicola (Genbank Accession No. AY198271) with 100% identity. These two organisms are taxonomically indistinguishable by rDNA sequences and are likely to be the same species (3). To our knowledge, this is the first report of P. pulveracea on Helleborus × hybridus in California and the United States. Lenten rose is commercially propagated by seed, which is a potential pathway for introduction of this pathogen. Mature plants are sold and shipped intra- and interstate as decorative flowering plants or nursery stock. The importance and economic impact of this disease is limited, but significant economic losses could occur during production.

References: (1) E. A. Gäumann. Beitr. Kryptogamenflora Schweiz 5:113, 1923. (2) G. Hall. Mycopathologia 126:57, 1994. (3) H. Voglmayr. Mycol. Res. 107:1132, 2003.
First Report of Mountain Hemlock Dwarf Mistletoe (Arceuthobium tsugense subsp. mertensianae) on Sugar Pine (Pinus lambertiana) from Oregon
Authors: Mathiasen R. , Daugherty C.
Published: February 2009

Mountain hemlock dwarf mistletoe (Arceuthobium tsugense (Rosendahl) G.N. Jones subsp. mertensianae Hawksw. & Nickrent, Viscaceae) commonly parasitizes mountain hemlock (Tsuga mertensiana (Bong.) Carr.) from the central Sierra Nevada Mountains to the southern Cascades in Oregon (1,3). It has also been reported to commonly parasitize whitebark pine (Pinus albicaulis Engelm.) and occasionally western white pine (P. monticola Dougl. ex D. Don) (1,4). In September of 2008, we found mountain hemlock dwarf mistletoe infecting two sugar pines (P. lambertiana Dougl.) 4.5 km north of Windigo Pass, Oregon (42°24′40″N, 123°35′26″W, elevation 2,710 m). One of the sugar pines was 63.5 cm (25 inches) in diameter and had three infections. The other tree was 22.4 cm (9 inches) in diameter, but had 17 infections, many with mistletoe plants that allowed identification of the mistletoe using published descriptions (1,2). Mountain hemlock dwarf mistletoe can be distinguished from sugar pine dwarf mistletoe (A. californicum Hawksw. & Wiens) by its smaller plant size (mean height 5 cm versus 8 cm) and plant color (green-brown versus green to yellow) (1,2). An area (site) of approximately 1 ha around the infected sugar pines was examined and none of the other sugar pines we observed (33 trees) were found to be infected. Because mountain hemlock dwarf mistletoe also occurs in the principal range of sugar pine in the Sierra Nevada Mountains, it may also parasitize this tree there. However, our observations in several mountain hemlock stands infested with mountain hemlock dwarf mistletoe in California have failed to uncover infection of sugar pine by this mistletoe. Therefore, we would tentatively classify sugar pine as a rare host of mountain hemlock dwarf mistletoe (1). Specimens of mountain hemlock dwarf mistletoe on sugar pine were collected and deposited at the Deaver Herbarium (ASC), Northern Arizona University, Flagstaff (Accession No. 87122). To our knowledge, this is the first report of mountain hemlock dwarf mistletoe parasitizing sugar pine.

References: (1) F. G. Hawksworth and D. Wiens. USDA For. Serv. Agric. Handb. 709, 1996. (2) F. G. Hawksworth et al. Novon 2:204, 1992. (3) R. L. Mathiasen and C. M. Daugherty. Novon 17:222, 2007. (4) R. L. Mathiasen and F. G. Hawksworth. For. Sci. 34:429, 1988.
First Report of Elm Yellows Phytoplasma Infecting Clover in China
Authors: Li Z. N. , Zheng X. , Wei H. J. , Yu X. Q. , Wu W. J. , Wu Y. F.
Published: February 2009

In the summer of 2008, phyllody and enlarged petioles resembling symptoms of phytoplasma infection were observed on clover (Trifolium repens) plants in lawns on the campus of Northwest A&F University. Typical phytoplasma-like bacteria were observed in the phloem cells when ultra-thin sections from leaf midrib tissues were examined with transmission electron microscopy. Nested PCR assays were used to verify the association of phytoplasma with the disease. Total DNA was extracted from the phloem of leaf midribs from 20 symptomatic plants and six symptomless plants using the modified CTAB method (1). Using the phytoplasma universal primer pair R16mF2/R16mR1 followed by specific primers R16F2n/R16R2 (4), PCR products of 1.4 and 1.2 kb were amplified, respectively, from symptomatic plants only. Jujube witches'-broom (JWB) and paulownia witches'-broom (PaWB) phytoplasma DNA samples served as controls and were used to study group relationships. After sequencing of the 16S rDNA fragment (GenBank Accession No. FJ436792), a BLAST search determined that the clover phytoplasma shared closest homology (99.6%) with JWB (GenBank Accession No. FJ154846) phytoplasmas compared with lesser identity (90.4%) with PaWB (GenBank Accession No. EF199937). Subsequent restriction fragment length polymorphism analysis of the PCR-amplified 1.2-kb 16S rDNA R16(1)F1/R1 fragment indicated that the phytoplasma associated with the disease belongs to subgroup 16SrV-B of the elm yellows phytoplasma group. Clover phyllody phytoplasma were previously reported to infect clover in Canada (GenBank Accession No. L33762) (3) and Italy (GenBank Accession No. X77482) (2). The phytoplasma reported here shared 86.7 and 90.0% identity with the clover phyllody phytoplasma above, respectively, much lower than that with Elm yellows phytoplasma group. To our knowledge, this is the first report of Elm yellows phytoplasma infecting clover in China.

References:(1) E. Angelini et al. Vitis 40:79, 2001. (2) G. Firrao et al. Eur. J. Plant Pathol. 102:817, 1996. (3) N. A. Harrison et al. Plant Pathol. 52:147, 2003. (4) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998.
First Report of Syringa oblata and S. reticulata Leafroll Disease in China
Authors: Li Z. N. , Min H. , Yan Y. , Zhao Z. , Wu W. J. , Wu Y. F.
Published: February 2009

Syringa oblata is an important ornamental tree widely grown in China. In September of 2008, S. oblata plants exhibiting symptoms of leafroll and yellowing were found in a garden on the Northwest A&F University campus. Samples were collected from this site. Total DNA was extracted from 0.5 g of phloem tissue from leaf midribs and stems of each sample. DNA samples were analyzed with a nested PCR assay using phytoplasma 16S rDNA universal primers R16mF2/R16mR1 followed by specific primers R16F2n/R16R2 (1), which amplified a 1,452- and 1,246-bp product, respectively. We tested all 30 lilac samples, 20 of which had symptoms of leafroll and yellowing. These produced the expected 1,452- and 1,246-bp PCR products In contrast, the remaining 10 samples from symptomless trees yielded no PCR products. We also surveyed another lilac variety (Syringa reticulata), which is widely grown on the campus, and tested 50 samples with the above method. Again, 1.4- and 1.2-kb PCR products were amplified from all 30 trees displaying leafroll and yellowing symptoms, but not from the other 20 samples from symptomless trees. A comparative analysis of sequences derived from the two hosts showed that the phytoplasmas infecting them were most similar (>99%) to paulownia witches'-broom (PaWB) phytoplasma (GenBank Accession No. EF199937). Restriction fragment length polymorphism (RFLP) analysis of the nested 1.2-kb 16S rDNA products with endonucleases AluI and MseI indicated that all symptomatic plants were infected by the phytoplasmas belonging to aster yellow group (16SrI) subgroup D (16SrI-D) PaWB phytoplasma (2). 16S rDNA sequence comparisons and RFLP analysis of the cloned 16S rDNA from S. oblata (GenBank Accession No. FJ445224) and S. reticulate (GenBank Accession No. FJ445225) indicated that the phytoplasmas infecting them were nearly identical (99.8% identity). To our knowledge, this is the first report of the presence of the phytoplasma associated with a leafroll disease of S. oblata and S. reticulata in China.

References: (1) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998.
First Report of Fusarium Wilt Caused by Fusarium oxysporum on Strawberry in Spain
Authors: Arroyo F. T. , Llergo Y. , Aguado A. , Romero F.
Published: February 2009

In the spring of 2007, wilted and dead strawberry plants (Fragaria × ananassa Duch. cvs. Camarosa and Ventana) were observed in a soilless culture system in Huelva, southwestern Spain. Approximately 8% of the plants in the field died. Isolations from necrotic crowns and roots and necrotic flowers were made on potato dextrose agar after disinfestation in 0.6% NaOCl for 30 s. Colonies with light purple mycelia and beige or orange reverse colony colors developed after 9 days of incubation at 25°C. Colonies produced abundant microconidia, macroconidia, and chlamydospores. Microconidia were hyaline and oval-ellipsoid to cylindrical (5.9 to 9.2 × 2.1 to 3.4 μm). Macroconidia were 3 to 5 septate and fusoid-subulate with a pedicellate base (28.8 to 37.3 × 3.2 to 4.3 μm). Morphology and growth matched descriptions of Fusarium oxysporum Schlechtend emend. Snyder & Hansen (2). A PCR assay for amplification of r-DNA using primers PFO2 and PFO3 established the identity of the isolate as F. oxysporum (1). To confirm the pathogenicity of the fungus, roots of 30-day-old strawberry cvs. Camarosa and Ventana (20 plants each) were inoculated by dipping the roots into a conidial suspension (107 conidia per ml) for 15 min. The inoculated plants were transplanted into plastic pots containing sterilized peat and maintained at 25°C and 100% relative humidity in a growth chamber with a daily 12-h photoperiod of fluorescent light. The pathogenicity test was conducted twice. Within 30 days, all inoculated plants developed wilt symptoms similar to that observed in the field and eventually 75% of the plants died. No symptoms were observed on plants dipped in distilled water. The fungus was successfully reisolated from crowns, roots, and necrotic flowers, fulfilling Koch's postulates. To our knowledge, this is the first report of the occurrence of Fusarium wilt caused by F. oxysporum on strawberry plants in Spain.

References: (1) V. Edel et al. Mycol. Res. 104:518, 2000. (2) W. C. Snyder and H. N. Hansen. Am. J. Bot. 27:64, 1940.
Evaluation of Alternative Decay Control Products for Control of Postharvest Rhizopus Soft Rot of Sweetpotatoes
Authors: Edmunds Brooke A. , Holmes Gerald J.
Published: February 2009

Postharvest Rhizopus soft rot of sweetpotato, caused by Rhizopus stolonifer, is managed by minimizing injuries incurred during harvesting and packing, curing roots immediately after harvest, and applying fungicide during packing. The United States sweetpotato industry relies heavily on a single fungicide (dicloran) to control Rhizopus soft rot, however, many markets (export, infant food, and organic) no longer allow dicloran residues. Dicloran is currently the only fungicide labeled for control of Rhizopus soft rot. Thirty-three products were tested in nine individual experiments over a 5-year period to identify alternative control products. The reduced-risk fungicides boscalid plus pyraclostrobin (Pristine) and fludioxonil (Scholar) significantly reduced Rhizopus soft rot and performed similarly to dicloran. The biological products Bio-Save 10LP and 11LP suppressed Rhizopus soft rot although results were variable among tests. Generally recognized as safe (GRAS) treatments were ineffective in controlling soft rot by our methods.

Accepted for publication 1 December 2008. Published 6 February 2009.
Protein Phosphatase 4 mediates localization of the Miranda complex during Drosophila neuroblast asymmetric divisions
Authors: Sousa-Nunes Rita , Chia William , Somers W. Greg
Published: February 2009

Asymmetric localization of cell fate determinants is a crucial step in neuroblast asymmetric divisions. Whereas several protein kinases have been shown to mediate this process, no protein phosphatase has so far been implicated. In a clonal screen of larval neuroblasts we identified the evolutionarily conserved Protein Phosphatase 4 (PP4) regulatory subunit PP4R3/Falafel (Flfl) as a key mediator specific for the localization of Miranda (Mira) and associated cell fate determinants during both interphase and mitosis. Flfl is predominantly nuclear during interphase/prophase and cytoplasmic after nuclear envelope breakdown. Analyses of nuclear excluded as well as membrane targeted versions of the protein suggest that the asymmetric cortical localization of Mira and its associated proteins during mitosis depends on cytoplasmic/membrane-associated Flfl, whereas nuclear Flfl is required to exclude the cell fate determinant Prospero (Pros), and consequently Mira, from the nucleus during interphase/prophase. Attenuating the function of either the catalytic subunit of PP4 (PP4C; Pp4-19C in Drosophila) or of another regulatory subunit, PP4R2 (PPP4R2r in Drosophila), leads to similar defects in the localization of Mira and associated proteins. Flfl is capable of directly interacting with Mira, and genetic analyses indicate that flfl acts in parallel to or downstream from the tumor suppressor lethal (2) giant larvae (lgl). Our findings suggest that Flfl may target PP4 to the MIra protein complex to facilitate dephosphorylation step(s) crucial for its cortical association/asymmetric localization.
A recombination execution checkpoint regulates the choice of homologous recombination pathway during DNA double-strand break repair
Authors: Jain Suvi , Sugawara Neal , Lydeard John , Vaze Moreshwar , Tanguy Le Gac Nicolas , Haber James E.
Published: February 2009

A DNA double-strand break (DSB) is repaired by gene conversion (GC) if both ends of the DSB share homology with an intact DNA sequence. However, if homology is limited to only one of the DSB ends, repair occurs by break-induced replication (BIR). It is not known how the homology status of the DSB ends is first assessed and what other parameters govern the choice between these repair pathways. Our data suggest that a “recombination execution checkpoint” (REC) regulates the choice of the homologous recombination pathway employed to repair a given DSB. This choice is made prior to the initiation of DNA synthesis, and is dependent on the relative position and orientation of the homologous sequences used for repair. The RecQ family helicase Sgs1 plays a key role in regulating the choice of the recombination pathway. Surprisingly, break repair and gap repair are fundamentally different processes, both kinetically and genetically, as Pol32 is required only for gap repair. We propose that the REC may have evolved to preserve genome integrity by promoting conservative repair, especially when a DSB occurs within a repeated sequence.
NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation
Authors: He Xin-Jian , Hsu Yi-Feng , Pontes Olga , Zhu Jianhua , Lu Jian , Bressan Ray A. , Pikaard Craig , Wang Co-Shine , Zhu Jian-Kang
Published: February 2009

RNA-directed DNA methylation (RdDM) is an RNAi-based mechanism for establishing transcriptional gene silencing in plants. The plant-specific RNA polymerases IV and V are required for the generation of 24-nucleotide (nt) siRNAs and for guiding sequence-specific DNA methylation by the siRNAs, respectively. However, unlike the extensively studied multisubunit Pol II, our current knowledge about Pol IV and Pol V is restricted to only the two largest subunits NRPD1a/NRPD1 and NRPD1b/NRPE1 and the one second-largest subunit NRPD2a. It is unclear whether other subunits may be required for the functioning of Pol IV and Pol V in RdDM. From a genetic screen for second-site suppressors of the DNA demethylase mutant ros1, we identified a new component (referred to as RDM2) as well as seven known components (NRPD1, NRPE1, NRPD2a, AGO4, HEN1, DRD1, and HDA6) of the RdDM pathway. The differential effects of the mutations on two mechanistically distinct transcriptional silencing reporters suggest that RDM2, NRPD1, NRPE1, NRPD2a, HEN1, and DRD1 function only in the siRNA-dependent pathway of transcriptional silencing, whereas HDA6 and AGO4 have roles in both siRNA-dependent and -independent pathways of transcriptional silencing. In the rdm2 mutants, DNA methylation and siRNA accumulation were reduced substantially at loci previously identified as endogenous targets of Pol IV and Pol V, including 5S rDNA, MEA-ISR, AtSN1, AtGP1, and AtMU1. The amino acid sequence of RDM2 is similar to that of RPB4 subunit of Pol II, but we show evidence that RDM2 has diverged significantly from RPB4 and cannot function in Pol II. An association of RDM2 with both NRPD1 and NRPE1 was observed by coimmunoprecipitation and coimmunolocalization assays. Our results show that RDM2/NRPD4/NRPE4 is a new component of the RdDM pathway in Arabidopsis and that it functions as part of Pol IV and Pol V.
Integration of transport-based models for phyllotaxis and midvein formation
Authors: Bayer Emmanuelle M. , Smith Richard S. , Mandel Therese , Nakayama Naomi , Sauer Michael , Prusinkiewicz Przemyslaw , Kuhlemeier Cris
Published: February 2009

The plant hormone auxin mediates developmental patterning by a mechanism that is based on active transport. In the shoot apical meristem, auxin gradients are thought to be set up through a feedback loop between auxin and the activity and polar localization of its transporter, the PIN1 protein. Two distinct molecular mechanisms for the subcellular polarization of PIN1 have been proposed. For leaf positioning (phyllotaxis), an “up-the-gradient” PIN1 polarization mechanism has been proposed, whereas the formation of vascular strands is thought to proceed by “with-the-flux” PIN1 polarization. These patterning mechanisms intersect during the initiation of the midvein, which raises the question of how two different PIN1 polarization mechanisms may work together. Our detailed analysis of PIN1 polarization during midvein initiation suggests that both mechanisms for PIN1 polarization operate simultaneously. Computer simulations of the resulting dual polarization model are able to reproduce the dynamics of observed PIN1 localization. In addition, the appearance of high auxin concentration in our simulations throughout the initiation of the midvein is consistent with experimental observation and offers an explanation for a long-standing criticism of the canalization hypothesis; namely, how both high flux and high concentration can occur simultaneously in emerging veins.
The importance of inter- and intramolecular base pairing for translation reinitiation on a eukaryotic bicistronic mRNA
Authors: Luttermann Christine , Meyers Gregor
Published: February 2009

Calicivirus structure proteins are expressed from a subgenomic mRNA with two overlapping cistrons. The first ORF of this RNA codes for the viral major capsid protein VP1, and the second for the minor capsid protein VP2. Translation of VP2 is mediated by a termination/reinitiation mechanism, which depends on an upstream sequence element of ∼70 nucleotides denoted “termination upstream ribosomal binding site” (TURBS). Two short sequence motifs within the TURBS were found to be essential for reinitiation. By a whole set of single site mutations and reciprocal base exchanges we demonstrate here for the first time conclusive evidence for the necessity of mRNA/18S rRNA hybridization for translation reinitiation in an eukaryotic system. Moreover, we show that motif 2 exhibits intramolecular hybridization with a complementary region upstream of motif 1, thus forming a secondary structure that positions post-termination ribosomes in an optimal distance to the VP2 start codon. Analysis of the essential elements of the TURBS led to a better understanding of the requirements for translation termination/reinitiation in eukaryotes.